Starting phenix.real_space_refine on Thu Jul 2 04:08:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8whz_37553/07_2026/8whz_37553.cif Found real_map, /net/cci-nas-00/data/ceres_data/8whz_37553/07_2026/8whz_37553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8whz_37553/07_2026/8whz_37553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8whz_37553/07_2026/8whz_37553.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8whz_37553/07_2026/8whz_37553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8whz_37553/07_2026/8whz_37553.map" } resolution = 3.93 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= -0.000 sd= 0.044 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 4173 2.51 5 N 1073 2.21 5 O 1230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6515 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: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 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, 57 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 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: 1.12, per 1000 atoms: 0.17 Number of scatterers: 6515 At special positions: 0 Unit cell: (75.97, 95.23, 114.49, 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 1230 8.00 N 1073 7.00 C 4173 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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: 0.39 Conformation dependent library (CDL) restraints added in 249.3 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, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.795A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix 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: 3.802A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.312A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.425A 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: 3.752A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.252A 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 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.918A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.743A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.685A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.642A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.653A 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 447 Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.240A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.753A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.827A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.532A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix 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: 3.894A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.806A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (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: 5.788A 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 352 removed outlier: 3.666A pdb=" N THR A 347 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 359 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.875A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.523A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) 315 hydrogen bonds defined for protein. 903 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: 0.72 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1864 1.33 - 1.46: 1357 1.46 - 1.58: 3422 1.58 - 1.70: 1 1.70 - 1.82: 58 Bond restraints: 6702 Sorted by residual: bond pdb=" C THR A 27 " pdb=" N PHE A 28 " ideal model delta sigma weight residual 1.335 1.292 0.043 1.30e-02 5.92e+03 1.12e+01 bond pdb=" N THR A 27 " pdb=" CA THR A 27 " ideal model delta sigma weight residual 1.459 1.421 0.038 1.17e-02 7.31e+03 1.08e+01 bond pdb=" CA ARG B 457 " pdb=" CB ARG B 457 " ideal model delta sigma weight residual 1.534 1.480 0.053 1.78e-02 3.16e+03 8.94e+00 bond pdb=" CA THR A 27 " pdb=" C THR A 27 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.24e-02 6.50e+03 6.85e+00 bond pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.30e+00 ... (remaining 6697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 8753 1.88 - 3.77: 312 3.77 - 5.65: 37 5.65 - 7.54: 6 7.54 - 9.42: 2 Bond angle restraints: 9110 Sorted by residual: angle pdb=" N LYS A 313 " pdb=" CA LYS A 313 " pdb=" C LYS A 313 " ideal model delta sigma weight residual 111.82 106.74 5.08 1.16e+00 7.43e-01 1.92e+01 angle pdb=" CA PRO B 384 " pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 112.00 106.33 5.67 1.40e+00 5.10e-01 1.64e+01 angle pdb=" N CYS A 498 " pdb=" CA CYS A 498 " pdb=" C CYS A 498 " ideal model delta sigma weight residual 110.44 105.84 4.60 1.20e+00 6.94e-01 1.47e+01 angle pdb=" CA ARG B 457 " pdb=" C ARG B 457 " pdb=" N LYS B 458 " ideal model delta sigma weight residual 115.61 120.89 -5.28 1.45e+00 4.76e-01 1.32e+01 angle pdb=" N VAL A 364 " pdb=" CA VAL A 364 " pdb=" C VAL A 364 " ideal model delta sigma weight residual 106.21 109.67 -3.46 1.07e+00 8.73e-01 1.05e+01 ... (remaining 9105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3628 17.95 - 35.90: 318 35.90 - 53.85: 58 53.85 - 71.80: 17 71.80 - 89.75: 8 Dihedral angle restraints: 4029 sinusoidal: 1705 harmonic: 2324 Sorted by residual: dihedral pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta harmonic sigma weight residual 180.00 143.36 36.64 0 5.00e+00 4.00e-02 5.37e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 134.85 -41.85 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 129.35 -36.35 1 1.00e+01 1.00e-02 1.87e+01 ... (remaining 4026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 705 0.049 - 0.097: 202 0.097 - 0.146: 54 0.146 - 0.194: 2 0.194 - 0.243: 1 Chirality restraints: 964 Sorted by residual: chirality pdb=" C1 NAG A 905 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 905 " pdb=" O5 NAG A 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA PRO B 384 " pdb=" N PRO B 384 " pdb=" C PRO B 384 " pdb=" CB PRO B 384 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" CG LEU B 492 " pdb=" CB LEU B 492 " pdb=" CD1 LEU B 492 " pdb=" CD2 LEU B 492 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 961 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 383 " -0.072 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO B 384 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 69 " -0.016 2.00e-02 2.50e+03 1.13e-02 3.22e+00 pdb=" CG TRP A 69 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 69 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 69 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 69 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 69 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 69 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 69 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 69 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 69 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 506 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO B 507 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 507 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 507 " 0.021 5.00e-02 4.00e+02 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 45 2.48 - 3.08: 4740 3.08 - 3.69: 10301 3.69 - 4.29: 14541 4.29 - 4.90: 22781 Nonbonded interactions: 52408 Sorted by model distance: nonbonded pdb=" O TYR B 421 " pdb=" CZ ARG B 457 " model vdw 1.873 3.270 nonbonded pdb=" O TYR B 421 " pdb=" NH1 ARG B 457 " model vdw 1.994 3.120 nonbonded pdb=" NH2 ARG B 454 " pdb=" CG ARG B 457 " model vdw 2.068 3.520 nonbonded pdb=" O LEU A 156 " pdb=" OH TYR A 252 " model vdw 2.142 3.040 nonbonded pdb=" CZ ARG B 454 " pdb=" NE ARG B 457 " model vdw 2.171 3.350 ... (remaining 52403 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 group one per residue 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.990 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:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 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 : 0.004 0.091 6717 Z= 0.208 Angle : 0.801 9.421 9142 Z= 0.458 Chirality : 0.047 0.243 964 Planarity : 0.006 0.105 1172 Dihedral : 14.476 89.752 2516 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 0.29 % Allowed : 0.29 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 are not related in a simple way. whole: -0.54 (0.30), residues: 787 helix: 0.61 (0.26), residues: 390 sheet: -0.55 (0.89), residues: 35 loop : -1.43 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 582 TYR 0.020 0.002 TYR A 454 PHE 0.014 0.002 PHE A 230 TRP 0.030 0.002 TRP A 69 HIS 0.004 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.21 ( 6702) covalent geometry : angle 0.79127 / 0.46 ( 9110) SS BOND : bond 0.00183 / 0.10 ( 7) SS BOND : angle 1.52970 / 0.78 ( 14) hydrogen bonds : bond 0.15190 / 10.16 ( 315) hydrogen bonds : angle 6.20077 / 4.55 ( 903) metal coordination : bond 0.00062 / 0.03 ( 2) link_NAG-ASN : bond 0.00435 / 0.30 ( 6) link_NAG-ASN : angle 2.70915 / 2.07 ( 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 203 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.6456 (mtp) cc_final: 0.6173 (mmm) REVERT: A 243 TYR cc_start: 0.9041 (t80) cc_final: 0.8645 (t80) REVERT: A 270 MET cc_start: 0.7170 (tpt) cc_final: 0.6919 (tpt) REVERT: A 333 LEU cc_start: 0.9346 (mt) cc_final: 0.9133 (mm) REVERT: A 408 MET cc_start: 0.8318 (mmp) cc_final: 0.8081 (mmt) REVERT: A 461 TRP cc_start: 0.8963 (m-10) cc_final: 0.8734 (m-10) REVERT: A 484 ILE cc_start: 0.8728 (mm) cc_final: 0.8256 (tp) REVERT: B 406 GLU cc_start: 0.8224 (mp0) cc_final: 0.8014 (mp0) outliers start: 2 outliers final: 1 residues processed: 202 average time/residue: 0.0639 time to fit residues: 16.7412 Evaluate side-chains 126 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN A 58 ASN A 60 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN B 417 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.143106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.114594 restraints weight = 16259.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.118120 restraints weight = 8994.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.120466 restraints weight = 6071.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.121920 restraints weight = 4653.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.123080 restraints weight = 3907.482| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6717 Z= 0.183 Angle : 0.709 8.167 9142 Z= 0.367 Chirality : 0.046 0.220 964 Planarity : 0.005 0.054 1172 Dihedral : 6.107 52.449 985 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.06 % Rotamer: Outliers : 2.59 % Allowed : 11.08 % Favored : 86.33 % 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 are not related in a simple way. whole: -0.35 (0.29), residues: 787 helix: 0.63 (0.25), residues: 406 sheet: -0.38 (0.79), residues: 42 loop : -1.25 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 582 TYR 0.021 0.002 TYR B 421 PHE 0.034 0.003 PHE B 375 TRP 0.022 0.002 TRP A 165 HIS 0.004 0.001 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 6702) covalent geometry : angle 0.69465 / 0.36 ( 9110) SS BOND : bond 0.00322 / 0.16 ( 7) SS BOND : angle 1.58203 / 0.76 ( 14) hydrogen bonds : bond 0.05229 / 3.31 ( 315) hydrogen bonds : angle 5.03972 / 3.69 ( 903) metal coordination : bond 0.00090 / 0.05 ( 2) link_NAG-ASN : bond 0.00415 / 0.26 ( 6) link_NAG-ASN : angle 3.03454 / 2.34 ( 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 149 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.8207 (mt) cc_final: 0.7739 (mm) REVERT: A 243 TYR cc_start: 0.8885 (t80) cc_final: 0.8652 (t80) REVERT: A 323 MET cc_start: 0.8273 (mmt) cc_final: 0.7276 (mmm) REVERT: A 360 MET cc_start: 0.8332 (ppp) cc_final: 0.7714 (ppp) REVERT: A 473 TRP cc_start: 0.7359 (m-10) cc_final: 0.7013 (m-10) REVERT: A 594 TRP cc_start: 0.8060 (t-100) cc_final: 0.7812 (t-100) REVERT: B 347 PHE cc_start: 0.6353 (m-80) cc_final: 0.5892 (m-80) outliers start: 18 outliers final: 9 residues processed: 141 average time/residue: 0.0646 time to fit residues: 12.5076 Evaluate side-chains 114 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 453 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 11 optimal weight: 0.0060 chunk 74 optimal weight: 0.0670 chunk 23 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.7936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN A 64 ASN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 472 GLN A 508 ASN B 417 ASN B 493 GLN B 505 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.141960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.113683 restraints weight = 15991.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.117024 restraints weight = 8953.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.119306 restraints weight = 6085.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.120648 restraints weight = 4699.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.121607 restraints weight = 3969.292| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6717 Z= 0.155 Angle : 0.660 7.054 9142 Z= 0.344 Chirality : 0.045 0.210 964 Planarity : 0.005 0.051 1172 Dihedral : 5.805 48.544 984 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.93 % Rotamer: Outliers : 2.59 % Allowed : 14.10 % Favored : 83.31 % 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 are not related in a simple way. whole: -0.28 (0.29), residues: 787 helix: 0.65 (0.25), residues: 406 sheet: 0.23 (0.83), residues: 42 loop : -1.24 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 582 TYR 0.015 0.002 TYR A 237 PHE 0.018 0.002 PHE A 369 TRP 0.018 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 6702) covalent geometry : angle 0.64844 / 0.34 ( 9110) SS BOND : bond 0.00329 / 0.16 ( 7) SS BOND : angle 1.58996 / 0.78 ( 14) hydrogen bonds : bond 0.04933 / 3.21 ( 315) hydrogen bonds : angle 4.89436 / 3.58 ( 903) metal coordination : bond 0.00119 / 0.06 ( 2) link_NAG-ASN : bond 0.00289 / 0.18 ( 6) link_NAG-ASN : angle 2.53734 / 1.94 ( 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 136 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.8112 (mt) cc_final: 0.7752 (mt) REVERT: A 180 TYR cc_start: 0.7949 (m-80) cc_final: 0.7424 (m-10) REVERT: A 243 TYR cc_start: 0.8823 (t80) cc_final: 0.8556 (t80) REVERT: A 287 GLN cc_start: 0.6875 (OUTLIER) cc_final: 0.6020 (pm20) REVERT: A 323 MET cc_start: 0.8395 (mmt) cc_final: 0.7134 (mmm) REVERT: A 333 LEU cc_start: 0.9025 (mt) cc_final: 0.8751 (mm) REVERT: A 366 MET cc_start: 0.8864 (ppp) cc_final: 0.7992 (ppp) REVERT: A 376 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7741 (tpt) REVERT: B 347 PHE cc_start: 0.6359 (m-80) cc_final: 0.6151 (m-80) outliers start: 18 outliers final: 7 residues processed: 130 average time/residue: 0.0617 time to fit residues: 10.8604 Evaluate side-chains 108 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 453 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 11 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.0770 chunk 17 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS A 378 HIS A 472 GLN A 508 ASN A 598 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.141358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.113535 restraints weight = 16351.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.116895 restraints weight = 9159.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.119191 restraints weight = 6212.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.120516 restraints weight = 4767.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.121140 restraints weight = 4025.666| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.845 6717 Z= 0.368 Angle : 0.622 6.975 9142 Z= 0.324 Chirality : 0.044 0.209 964 Planarity : 0.005 0.047 1172 Dihedral : 5.432 39.662 984 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 2.73 % Allowed : 16.26 % 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 are not related in a simple way. whole: -0.01 (0.29), residues: 787 helix: 0.88 (0.25), residues: 401 sheet: 0.90 (0.82), residues: 40 loop : -1.17 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.013 0.001 TYR A 237 PHE 0.032 0.002 PHE B 375 TRP 0.025 0.001 TRP A 594 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 6702) covalent geometry : angle 0.61227 / 0.32 ( 9110) SS BOND : bond 0.00239 / 0.16 ( 7) SS BOND : angle 1.58194 / 0.73 ( 14) hydrogen bonds : bond 0.04605 / 3.02 ( 315) hydrogen bonds : angle 4.71482 / 3.44 ( 903) metal coordination : bond 0.59718 / 28.44 ( 2) link_NAG-ASN : bond 0.00265 / 0.15 ( 6) link_NAG-ASN : angle 2.17975 / 1.64 ( 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 129 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.8247 (t-100) cc_final: 0.7632 (t60) REVERT: A 366 MET cc_start: 0.8845 (ppp) cc_final: 0.8001 (ppp) REVERT: A 406 GLU cc_start: 0.8394 (tp30) cc_final: 0.8175 (mm-30) REVERT: A 441 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8393 (ttpp) REVERT: A 462 MET cc_start: 0.8438 (ptp) cc_final: 0.7955 (mtm) REVERT: A 467 GLU cc_start: 0.8104 (pm20) cc_final: 0.6824 (pm20) REVERT: B 347 PHE cc_start: 0.6093 (m-80) cc_final: 0.5562 (m-80) REVERT: B 349 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.8213 (p) REVERT: B 406 GLU cc_start: 0.7814 (mp0) cc_final: 0.7514 (mp0) outliers start: 19 outliers final: 11 residues processed: 122 average time/residue: 0.0613 time to fit residues: 10.2325 Evaluate side-chains 107 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 380 GLN A 472 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.138815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.110865 restraints weight = 16274.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.114048 restraints weight = 9127.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.116240 restraints weight = 6236.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.117689 restraints weight = 4818.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.118682 restraints weight = 4032.135| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6717 Z= 0.154 Angle : 0.628 8.938 9142 Z= 0.330 Chirality : 0.044 0.201 964 Planarity : 0.005 0.045 1172 Dihedral : 5.336 37.958 984 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 3.60 % Allowed : 17.84 % Favored : 78.56 % 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 are not related in a simple way. whole: -0.17 (0.29), residues: 787 helix: 0.78 (0.25), residues: 406 sheet: 0.45 (0.96), residues: 32 loop : -1.24 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 346 TYR 0.022 0.002 TYR A 243 PHE 0.019 0.002 PHE B 490 TRP 0.027 0.002 TRP A 594 HIS 0.005 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 6702) covalent geometry : angle 0.61993 / 0.33 ( 9110) SS BOND : bond 0.00598 / 0.30 ( 7) SS BOND : angle 1.48413 / 0.86 ( 14) hydrogen bonds : bond 0.04757 / 3.08 ( 315) hydrogen bonds : angle 4.69895 / 3.42 ( 903) metal coordination : bond 0.01077 / 0.54 ( 2) link_NAG-ASN : bond 0.00185 / 0.10 ( 6) link_NAG-ASN : angle 2.07154 / 1.53 ( 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 134 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.8237 (t-100) cc_final: 0.7893 (t60) REVERT: A 190 MET cc_start: 0.8033 (ptp) cc_final: 0.7819 (ptp) REVERT: A 249 MET cc_start: 0.8390 (mtp) cc_final: 0.7603 (mpp) REVERT: A 287 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6393 (pm20) REVERT: A 323 MET cc_start: 0.8385 (mmm) cc_final: 0.7121 (mmm) REVERT: A 366 MET cc_start: 0.8874 (ppp) cc_final: 0.8007 (ppp) REVERT: A 376 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7641 (tpt) REVERT: A 441 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8451 (ttpp) REVERT: B 347 PHE cc_start: 0.6223 (m-80) cc_final: 0.5927 (m-80) REVERT: B 349 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8352 (p) REVERT: B 406 GLU cc_start: 0.7887 (mp0) cc_final: 0.7552 (mp0) outliers start: 25 outliers final: 17 residues processed: 124 average time/residue: 0.0585 time to fit residues: 9.9944 Evaluate side-chains 117 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 0.0980 chunk 63 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.0040 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 472 GLN B 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.139908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.112100 restraints weight = 16216.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.115415 restraints weight = 8985.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.117654 restraints weight = 6083.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.118999 restraints weight = 4650.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.120144 restraints weight = 3909.568| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6717 Z= 0.130 Angle : 0.617 6.638 9142 Z= 0.323 Chirality : 0.044 0.199 964 Planarity : 0.004 0.051 1172 Dihedral : 5.025 36.853 984 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 2.88 % Allowed : 20.72 % Favored : 76.40 % 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 are not related in a simple way. whole: -0.03 (0.29), residues: 787 helix: 0.86 (0.25), residues: 403 sheet: 0.88 (0.77), residues: 40 loop : -1.19 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 457 TYR 0.023 0.001 TYR A 243 PHE 0.031 0.001 PHE B 375 TRP 0.040 0.002 TRP A 473 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 6702) covalent geometry : angle 0.60906 / 0.32 ( 9110) SS BOND : bond 0.00365 / 0.18 ( 7) SS BOND : angle 1.66392 / 0.81 ( 14) hydrogen bonds : bond 0.04450 / 2.91 ( 315) hydrogen bonds : angle 4.57972 / 3.35 ( 903) metal coordination : bond 0.00026 / 0.01 ( 2) link_NAG-ASN : bond 0.00226 / 0.12 ( 6) link_NAG-ASN : angle 1.83954 / 1.35 ( 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 130 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8959 (m110) cc_final: 0.8563 (m-40) REVERT: A 163 TRP cc_start: 0.8385 (t-100) cc_final: 0.8152 (t60) REVERT: A 249 MET cc_start: 0.8385 (mtp) cc_final: 0.7577 (mpp) REVERT: A 287 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6492 (pm20) REVERT: A 323 MET cc_start: 0.8424 (mmm) cc_final: 0.6974 (mmm) REVERT: A 366 MET cc_start: 0.8845 (ppp) cc_final: 0.8095 (ppp) REVERT: A 376 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7623 (tpt) REVERT: A 406 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8499 (mm-30) REVERT: A 441 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8419 (ttpp) REVERT: A 461 TRP cc_start: 0.9018 (m-10) cc_final: 0.8769 (m-10) REVERT: A 467 GLU cc_start: 0.8443 (pm20) cc_final: 0.7968 (pm20) REVERT: B 347 PHE cc_start: 0.6249 (m-80) cc_final: 0.5958 (m-80) REVERT: B 349 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8097 (p) REVERT: B 406 GLU cc_start: 0.7882 (mp0) cc_final: 0.7618 (mp0) outliers start: 20 outliers final: 9 residues processed: 122 average time/residue: 0.0501 time to fit residues: 8.7356 Evaluate side-chains 110 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 472 GLN ** B 439 ASN ** 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 = 0.4010 r_free = 0.4010 target = 0.138431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.110854 restraints weight = 16059.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.113959 restraints weight = 9147.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.116103 restraints weight = 6296.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.117426 restraints weight = 4866.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.118492 restraints weight = 4104.648| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6717 Z= 0.133 Angle : 0.611 8.694 9142 Z= 0.321 Chirality : 0.044 0.194 964 Planarity : 0.004 0.045 1172 Dihedral : 4.958 36.033 984 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 3.88 % Allowed : 20.86 % Favored : 75.25 % 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 are not related in a simple way. whole: -0.07 (0.29), residues: 787 helix: 0.83 (0.25), residues: 409 sheet: 0.82 (0.76), residues: 41 loop : -1.24 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 457 TYR 0.024 0.002 TYR A 243 PHE 0.023 0.001 PHE A 452 TRP 0.037 0.002 TRP A 594 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 6702) covalent geometry : angle 0.60413 / 0.32 ( 9110) SS BOND : bond 0.00378 / 0.19 ( 7) SS BOND : angle 1.58229 / 0.73 ( 14) hydrogen bonds : bond 0.04443 / 2.89 ( 315) hydrogen bonds : angle 4.52872 / 3.31 ( 903) metal coordination : bond 0.00036 / 0.02 ( 2) link_NAG-ASN : bond 0.00174 / 0.09 ( 6) link_NAG-ASN : angle 1.75595 / 1.27 ( 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 125 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8965 (m110) cc_final: 0.8558 (m-40) REVERT: A 152 MET cc_start: 0.7000 (mmt) cc_final: 0.6453 (mmm) REVERT: A 287 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.6661 (pm20) REVERT: A 306 ARG cc_start: 0.8433 (ttp-170) cc_final: 0.8168 (ttp-170) REVERT: A 323 MET cc_start: 0.8356 (mmm) cc_final: 0.6971 (mmm) REVERT: A 366 MET cc_start: 0.8774 (ppp) cc_final: 0.8048 (ppp) REVERT: A 376 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7702 (tpt) REVERT: A 406 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8577 (mm-30) REVERT: A 441 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8483 (ttpp) REVERT: A 560 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8736 (mt) outliers start: 27 outliers final: 15 residues processed: 117 average time/residue: 0.0476 time to fit residues: 8.0547 Evaluate side-chains 112 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 67 optimal weight: 0.0060 chunk 4 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 472 GLN ** B 439 ASN ** 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 = 0.4021 r_free = 0.4021 target = 0.139050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.111273 restraints weight = 16280.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.114429 restraints weight = 9309.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.116588 restraints weight = 6404.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.117967 restraints weight = 4965.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.118849 restraints weight = 4175.615| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.6487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6717 Z= 0.127 Angle : 0.615 7.898 9142 Z= 0.320 Chirality : 0.044 0.193 964 Planarity : 0.005 0.050 1172 Dihedral : 4.828 34.853 984 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 3.17 % Allowed : 22.16 % Favored : 74.68 % 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 are not related in a simple way. whole: -0.02 (0.29), residues: 787 helix: 0.94 (0.26), residues: 402 sheet: 0.60 (0.78), residues: 43 loop : -1.24 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 457 TYR 0.025 0.001 TYR A 243 PHE 0.032 0.002 PHE B 375 TRP 0.035 0.002 TRP A 594 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 6702) covalent geometry : angle 0.60934 / 0.32 ( 9110) SS BOND : bond 0.00358 / 0.18 ( 7) SS BOND : angle 1.34349 / 0.66 ( 14) hydrogen bonds : bond 0.04334 / 2.80 ( 315) hydrogen bonds : angle 4.47869 / 3.29 ( 903) metal coordination : bond 0.00055 / 0.03 ( 2) link_NAG-ASN : bond 0.00182 / 0.09 ( 6) link_NAG-ASN : angle 1.66180 / 1.19 ( 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 126 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.9006 (m110) cc_final: 0.8569 (m-40) REVERT: A 152 MET cc_start: 0.6851 (mmt) cc_final: 0.6488 (mmm) REVERT: A 249 MET cc_start: 0.8140 (mtp) cc_final: 0.7128 (mpp) REVERT: A 287 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6588 (pm20) REVERT: A 306 ARG cc_start: 0.8425 (ttp-170) cc_final: 0.8157 (ttp-170) REVERT: A 323 MET cc_start: 0.8328 (mmm) cc_final: 0.7039 (mmm) REVERT: A 366 MET cc_start: 0.8745 (ppp) cc_final: 0.8040 (ppp) REVERT: A 376 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7696 (tpt) REVERT: A 406 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8606 (mm-30) REVERT: A 441 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8601 (ttpp) REVERT: A 461 TRP cc_start: 0.8984 (m-10) cc_final: 0.8723 (m-10) REVERT: A 560 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8740 (mt) outliers start: 22 outliers final: 15 residues processed: 119 average time/residue: 0.0532 time to fit residues: 8.9695 Evaluate side-chains 114 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 472 GLN ** B 439 ASN ** 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 = 0.4005 r_free = 0.4005 target = 0.137609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.110105 restraints weight = 16262.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.113215 restraints weight = 9156.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.115358 restraints weight = 6259.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.116533 restraints weight = 4831.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.117453 restraints weight = 4089.027| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.6698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6717 Z= 0.134 Angle : 0.632 8.615 9142 Z= 0.330 Chirality : 0.043 0.189 964 Planarity : 0.004 0.050 1172 Dihedral : 4.844 34.247 984 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 3.31 % Allowed : 22.88 % Favored : 73.81 % 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 are not related in a simple way. whole: 0.03 (0.29), residues: 787 helix: 1.00 (0.26), residues: 401 sheet: 0.99 (0.77), residues: 41 loop : -1.29 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 457 TYR 0.023 0.002 TYR A 243 PHE 0.015 0.001 PHE A 452 TRP 0.030 0.002 TRP A 594 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 6702) covalent geometry : angle 0.62749 / 0.33 ( 9110) SS BOND : bond 0.00320 / 0.16 ( 7) SS BOND : angle 1.19740 / 0.61 ( 14) hydrogen bonds : bond 0.04360 / 2.80 ( 315) hydrogen bonds : angle 4.52964 / 3.33 ( 903) metal coordination : bond 0.00066 / 0.03 ( 2) link_NAG-ASN : bond 0.00168 / 0.08 ( 6) link_NAG-ASN : angle 1.62438 / 1.15 ( 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 126 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.9028 (m110) cc_final: 0.8707 (m-40) REVERT: A 152 MET cc_start: 0.6983 (mmt) cc_final: 0.6628 (mmm) REVERT: A 287 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6720 (pm20) REVERT: A 306 ARG cc_start: 0.8456 (ttp-170) cc_final: 0.8118 (ttp-170) REVERT: A 323 MET cc_start: 0.8326 (mmm) cc_final: 0.7073 (mmm) REVERT: A 366 MET cc_start: 0.8746 (ppp) cc_final: 0.8038 (ppp) REVERT: A 376 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7604 (tpt) REVERT: A 406 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8612 (mm-30) REVERT: A 441 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8610 (ttpp) REVERT: A 461 TRP cc_start: 0.9034 (m-10) cc_final: 0.8786 (m-10) REVERT: A 560 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8764 (mt) REVERT: A 591 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8587 (tt) REVERT: B 492 LEU cc_start: 0.7583 (mt) cc_final: 0.7380 (mt) outliers start: 23 outliers final: 16 residues processed: 118 average time/residue: 0.0449 time to fit residues: 7.8370 Evaluate side-chains 117 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 0.0000 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 472 GLN A 598 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.137484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.110087 restraints weight = 16122.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.113202 restraints weight = 9098.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.115317 restraints weight = 6227.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.116574 restraints weight = 4824.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.117523 restraints weight = 4078.394| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.6876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6717 Z= 0.136 Angle : 0.642 9.213 9142 Z= 0.336 Chirality : 0.044 0.187 964 Planarity : 0.004 0.048 1172 Dihedral : 4.819 33.591 984 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 3.45 % Allowed : 23.17 % Favored : 73.38 % 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 are not related in a simple way. whole: 0.09 (0.30), residues: 787 helix: 1.04 (0.26), residues: 398 sheet: 1.04 (0.78), residues: 41 loop : -1.23 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 457 TYR 0.028 0.001 TYR A 243 PHE 0.020 0.001 PHE A 592 TRP 0.065 0.002 TRP A 594 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 6702) covalent geometry : angle 0.63798 / 0.34 ( 9110) SS BOND : bond 0.00314 / 0.16 ( 7) SS BOND : angle 1.13081 / 0.60 ( 14) hydrogen bonds : bond 0.04510 / 2.88 ( 315) hydrogen bonds : angle 4.59112 / 3.39 ( 903) metal coordination : bond 0.00071 / 0.03 ( 2) link_NAG-ASN : bond 0.00169 / 0.08 ( 6) link_NAG-ASN : angle 1.59596 / 1.11 ( 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 126 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7851 (ppp) cc_final: 0.7370 (ppp) REVERT: A 121 ASN cc_start: 0.9018 (m110) cc_final: 0.8697 (m-40) REVERT: A 152 MET cc_start: 0.6904 (mmt) cc_final: 0.6680 (mmm) REVERT: A 287 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6693 (pm20) REVERT: A 306 ARG cc_start: 0.8430 (ttp-170) cc_final: 0.8096 (ttp-170) REVERT: A 323 MET cc_start: 0.8316 (mmm) cc_final: 0.7183 (mmm) REVERT: A 366 MET cc_start: 0.8718 (ppp) cc_final: 0.8050 (ppp) REVERT: A 376 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7606 (tpt) REVERT: A 406 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8636 (mm-30) REVERT: A 441 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8601 (ttpp) REVERT: A 461 TRP cc_start: 0.9001 (m-10) cc_final: 0.8737 (m-10) REVERT: A 480 MET cc_start: 0.8704 (mtp) cc_final: 0.8410 (mtp) REVERT: A 512 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8353 (t80) outliers start: 24 outliers final: 18 residues processed: 119 average time/residue: 0.0505 time to fit residues: 8.6963 Evaluate side-chains 119 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 472 GLN ** B 439 ASN ** 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 = 0.3980 r_free = 0.3980 target = 0.135924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108381 restraints weight = 16087.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.111422 restraints weight = 9220.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.113502 restraints weight = 6348.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.114732 restraints weight = 4933.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.115730 restraints weight = 4181.400| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.7080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6717 Z= 0.151 Angle : 0.661 10.088 9142 Z= 0.344 Chirality : 0.045 0.183 964 Planarity : 0.005 0.049 1172 Dihedral : 4.944 34.014 984 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 3.74 % Allowed : 23.17 % Favored : 73.09 % 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 are not related in a simple way. whole: 0.11 (0.30), residues: 787 helix: 1.06 (0.26), residues: 398 sheet: 0.99 (0.78), residues: 41 loop : -1.21 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 457 TYR 0.026 0.002 TYR A 243 PHE 0.021 0.002 PHE A 592 TRP 0.076 0.002 TRP A 594 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 6702) covalent geometry : angle 0.65615 / 0.34 ( 9110) SS BOND : bond 0.00301 / 0.15 ( 7) SS BOND : angle 1.22294 / 0.66 ( 14) hydrogen bonds : bond 0.04690 / 2.99 ( 315) hydrogen bonds : angle 4.60872 / 3.40 ( 903) metal coordination : bond 0.00084 / 0.04 ( 2) link_NAG-ASN : bond 0.00179 / 0.10 ( 6) link_NAG-ASN : angle 1.67704 / 1.15 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1115.61 seconds wall clock time: 19 minutes 55.64 seconds (1195.64 seconds total)