Starting phenix.real_space_refine on Tue May 13 13:23:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xn2_38495/05_2025/8xn2_38495.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xn2_38495/05_2025/8xn2_38495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xn2_38495/05_2025/8xn2_38495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xn2_38495/05_2025/8xn2_38495.map" model { file = "/net/cci-nas-00/data/ceres_data/8xn2_38495/05_2025/8xn2_38495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xn2_38495/05_2025/8xn2_38495.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4872 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4175 2.51 5 N 1074 2.21 5 O 1240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6527 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4872 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} bond proxies already assigned to first conformer: 4987 Chain: "B" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1545 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 34 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 34 " occ=0.50 Time building chain proxies: 8.89, per 1000 atoms: 1.36 Number of scatterers: 6527 At special positions: 0 Unit cell: (84.032, 78.376, 117.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1240 8.00 N 1074 7.00 C 4175 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 103 " " NAG A 703 " - " ASN A 432 " " NAG A 704 " - " ASN A 546 " " NAG A 705 " - " ASN A 322 " " NAG C 1 " - " ASN A 90 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 706 " pdb="ZN ZN A 706 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 706 " - pdb=" NE2 HIS A 378 " 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 56.6% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.985A pdb=" N ASP A 38 " --> pdb=" O AHIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.693A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) 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 92 through 101 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.072A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.288A 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 220 through 252 removed outlier: 3.605A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.644A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.646A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.511A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.077A 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 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.185A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.580A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 547 through 561 removed outlier: 3.525A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.617A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.760A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 134 removed outlier: 6.967A pdb=" N GLU A 140 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.195A 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: 6.467A 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: 3.526A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.680A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 925 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2068 1.34 - 1.46: 1419 1.46 - 1.58: 3167 1.58 - 1.70: 0 1.70 - 1.81: 58 Bond restraints: 6712 Sorted by residual: bond pdb=" C ASN A 33 " pdb=" N BHIS A 34 " ideal model delta sigma weight residual 1.335 1.393 -0.058 1.38e-02 5.25e+03 1.75e+01 bond pdb=" N THR A 20 " pdb=" CA THR A 20 " ideal model delta sigma weight residual 1.454 1.486 -0.031 1.15e-02 7.56e+03 7.42e+00 bond pdb=" N GLN A 102 " pdb=" CA GLN A 102 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.42e-02 4.96e+03 5.47e+00 bond pdb=" N LEU A 91 " pdb=" CA LEU A 91 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.03e+00 bond pdb=" C BHIS A 34 " pdb=" N GLU A 35 " ideal model delta sigma weight residual 1.334 1.303 0.032 1.43e-02 4.89e+03 4.92e+00 ... (remaining 6707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 8965 2.09 - 4.18: 141 4.18 - 6.27: 20 6.27 - 8.36: 1 8.36 - 10.45: 1 Bond angle restraints: 9128 Sorted by residual: angle pdb=" C ILE A 21 " pdb=" N GLU A 22 " pdb=" CA GLU A 22 " ideal model delta sigma weight residual 120.29 109.84 10.45 1.42e+00 4.96e-01 5.42e+01 angle pdb=" C ASN A 103 " pdb=" N GLY A 104 " pdb=" CA GLY A 104 " ideal model delta sigma weight residual 120.14 115.08 5.06 1.25e+00 6.40e-01 1.64e+01 angle pdb=" C ASN A 33 " pdb=" N BHIS A 34 " pdb=" CA BHIS A 34 " ideal model delta sigma weight residual 120.31 114.77 5.54 1.52e+00 4.33e-01 1.33e+01 angle pdb=" N GLN A 102 " pdb=" CA GLN A 102 " pdb=" C GLN A 102 " ideal model delta sigma weight residual 113.19 108.90 4.29 1.19e+00 7.06e-01 1.30e+01 angle pdb=" O ASN A 33 " pdb=" C ASN A 33 " pdb=" N BHIS A 34 " ideal model delta sigma weight residual 122.07 125.67 -3.60 1.03e+00 9.43e-01 1.22e+01 ... (remaining 9123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 3804 21.15 - 42.31: 212 42.31 - 63.46: 24 63.46 - 84.61: 22 84.61 - 105.77: 5 Dihedral angle restraints: 4067 sinusoidal: 1739 harmonic: 2328 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -141.72 55.72 1 1.00e+01 1.00e-02 4.19e+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 93.00 125.90 -32.90 1 1.00e+01 1.00e-02 1.54e+01 dihedral pdb=" CA SER B 494 " pdb=" C SER B 494 " pdb=" N TYR B 495 " pdb=" CA TYR B 495 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 973 0.169 - 0.338: 4 0.338 - 0.508: 0 0.508 - 0.677: 1 0.677 - 0.846: 1 Chirality restraints: 979 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.08e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 2.85e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.55 -0.85 2.00e-01 2.50e+01 1.79e+01 ... (remaining 976 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.338 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG C 1 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.048 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.510 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 703 " -0.307 2.00e-02 2.50e+03 2.64e-01 8.68e+02 pdb=" C7 NAG A 703 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A 703 " -0.001 2.00e-02 2.50e+03 pdb=" N2 NAG A 703 " 0.450 2.00e-02 2.50e+03 pdb=" O7 NAG A 703 " -0.214 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 702 " 0.154 2.00e-02 2.50e+03 1.27e-01 2.02e+02 pdb=" C7 NAG A 702 " -0.042 2.00e-02 2.50e+03 pdb=" C8 NAG A 702 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG A 702 " -0.205 2.00e-02 2.50e+03 pdb=" O7 NAG A 702 " -0.021 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 704 2.74 - 3.28: 6529 3.28 - 3.82: 11456 3.82 - 4.36: 13312 4.36 - 4.90: 22587 Nonbonded interactions: 54588 Sorted by model distance: nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.206 3.040 nonbonded pdb=" OG SER B 514 " pdb=" OE2 GLU B 516 " model vdw 2.267 3.040 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 706 " model vdw 2.275 2.230 nonbonded pdb=" NH1 ARG B 457 " pdb=" O SER B 459 " model vdw 2.288 3.120 nonbonded pdb=" NE2 HIS A 374 " pdb=" OE1 GLU A 402 " model vdw 2.307 3.120 ... (remaining 54583 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.950 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6033 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 : 0.005 0.149 6729 Z= 0.222 Angle : 0.743 19.143 9166 Z= 0.388 Chirality : 0.056 0.846 979 Planarity : 0.013 0.292 1172 Dihedral : 14.752 105.768 2552 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.30), residues: 790 helix: 1.86 (0.27), residues: 394 sheet: 1.73 (0.79), residues: 37 loop : -0.30 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.011 0.002 HIS A 378 PHE 0.016 0.001 PHE A 592 TYR 0.021 0.001 TYR A 385 ARG 0.001 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.01706 ( 6) link_NAG-ASN : angle 6.51682 ( 18) link_BETA1-4 : bond 0.04267 ( 2) link_BETA1-4 : angle 10.45151 ( 6) hydrogen bonds : bond 0.12362 ( 318) hydrogen bonds : angle 5.40144 ( 925) metal coordination : bond 0.14462 ( 2) SS BOND : bond 0.00122 ( 7) SS BOND : angle 0.46252 ( 14) covalent geometry : bond 0.00364 ( 6712) covalent geometry : angle 0.63086 ( 9128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLN cc_start: 0.7381 (mt0) cc_final: 0.7016 (mt0) REVERT: A 62 MET cc_start: 0.6792 (ttt) cc_final: 0.6481 (ttp) REVERT: A 63 ASN cc_start: 0.7254 (m-40) cc_final: 0.6920 (m-40) REVERT: A 69 TRP cc_start: 0.7343 (t-100) cc_final: 0.6981 (t-100) REVERT: A 79 LEU cc_start: 0.7823 (mt) cc_final: 0.7617 (tt) REVERT: A 166 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6495 (tm-30) REVERT: A 181 GLU cc_start: 0.6650 (mt-10) cc_final: 0.5868 (mm-30) REVERT: A 249 MET cc_start: 0.6946 (ttm) cc_final: 0.6529 (tmt) REVERT: A 309 LYS cc_start: 0.6899 (mmtt) cc_final: 0.6684 (tppp) REVERT: A 315 PHE cc_start: 0.7713 (m-80) cc_final: 0.7433 (m-80) REVERT: A 320 LEU cc_start: 0.7688 (mt) cc_final: 0.7375 (mp) REVERT: A 324 THR cc_start: 0.6941 (m) cc_final: 0.6660 (p) REVERT: A 327 PHE cc_start: 0.6935 (t80) cc_final: 0.6700 (t80) REVERT: A 330 ASN cc_start: 0.7527 (m-40) cc_final: 0.6911 (m110) REVERT: A 349 TRP cc_start: 0.7630 (m100) cc_final: 0.7236 (m100) REVERT: A 362 THR cc_start: 0.6829 (m) cc_final: 0.6107 (m) REVERT: A 382 ASP cc_start: 0.7116 (m-30) cc_final: 0.6681 (m-30) REVERT: A 385 TYR cc_start: 0.7179 (p90) cc_final: 0.6884 (p90) REVERT: A 400 PHE cc_start: 0.7039 (m-10) cc_final: 0.6772 (m-80) REVERT: A 408 MET cc_start: 0.7077 (mmt) cc_final: 0.6822 (mmt) REVERT: A 441 LYS cc_start: 0.6470 (tttt) cc_final: 0.6172 (ttpp) REVERT: A 462 MET cc_start: 0.6474 (mtt) cc_final: 0.5524 (mtm) REVERT: A 465 LYS cc_start: 0.7999 (mttp) cc_final: 0.7461 (mttt) REVERT: A 467 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6478 (mp0) REVERT: A 477 TRP cc_start: 0.5159 (t-100) cc_final: 0.4787 (t-100) REVERT: A 480 MET cc_start: 0.6110 (mtm) cc_final: 0.5858 (mtp) REVERT: A 482 ARG cc_start: 0.6322 (ttm170) cc_final: 0.5996 (ttm-80) REVERT: A 489 GLU cc_start: 0.6397 (pm20) cc_final: 0.5907 (pm20) REVERT: A 499 ASP cc_start: 0.7568 (m-30) cc_final: 0.7315 (m-30) REVERT: A 559 ARG cc_start: 0.7481 (ptm-80) cc_final: 0.7217 (ppp80) REVERT: A 562 LYS cc_start: 0.7612 (mtpt) cc_final: 0.7326 (mtmt) REVERT: A 577 LYS cc_start: 0.7744 (mttp) cc_final: 0.7203 (mtpt) REVERT: A 582 ARG cc_start: 0.7110 (tpp80) cc_final: 0.6818 (tpm-80) REVERT: A 603 PHE cc_start: 0.6363 (t80) cc_final: 0.5897 (t80) REVERT: A 606 TRP cc_start: 0.7584 (p90) cc_final: 0.7199 (p90) REVERT: A 611 SER cc_start: 0.7182 (m) cc_final: 0.6863 (p) REVERT: B 407 VAL cc_start: 0.7943 (t) cc_final: 0.7450 (m) REVERT: B 414 GLN cc_start: 0.7559 (mm110) cc_final: 0.7240 (mm110) REVERT: B 424 LYS cc_start: 0.7256 (tppt) cc_final: 0.6979 (tttt) REVERT: B 468 ILE cc_start: 0.7771 (pt) cc_final: 0.7349 (mt) REVERT: B 512 VAL cc_start: 0.7038 (t) cc_final: 0.6815 (p) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.9837 time to fit residues: 237.9008 Evaluate side-chains 178 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 39 optimal weight: 0.1980 chunk 31 optimal weight: 0.4980 chunk 61 optimal weight: 0.0970 chunk 23 optimal weight: 0.0870 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 70 optimal weight: 0.0020 overall best weight: 0.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A A 117 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN A 397 ASN A 493 HIS B 343 ASN B 437 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.165228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.144820 restraints weight = 19815.830| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 3.35 r_work: 0.3842 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3840 r_free = 0.3840 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3840 r_free = 0.3840 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6729 Z= 0.143 Angle : 0.659 12.315 9166 Z= 0.322 Chirality : 0.045 0.229 979 Planarity : 0.004 0.042 1172 Dihedral : 8.482 75.003 1026 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.73 % Allowed : 12.37 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.30), residues: 790 helix: 1.76 (0.26), residues: 391 sheet: 0.81 (0.71), residues: 49 loop : -0.12 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.005 0.001 HIS A 378 PHE 0.027 0.002 PHE B 497 TYR 0.028 0.002 TYR A 385 ARG 0.003 0.000 ARG A 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 6) link_NAG-ASN : angle 2.81024 ( 18) link_BETA1-4 : bond 0.01475 ( 2) link_BETA1-4 : angle 7.17458 ( 6) hydrogen bonds : bond 0.04933 ( 318) hydrogen bonds : angle 4.70685 ( 925) metal coordination : bond 0.00651 ( 2) SS BOND : bond 0.00221 ( 7) SS BOND : angle 0.48495 ( 14) covalent geometry : bond 0.00309 ( 6712) covalent geometry : angle 0.62164 ( 9128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 63 ASN cc_start: 0.7947 (m-40) cc_final: 0.7674 (m-40) REVERT: A 68 LYS cc_start: 0.8317 (ttmm) cc_final: 0.8065 (ttmm) REVERT: A 69 TRP cc_start: 0.7948 (t-100) cc_final: 0.7707 (t-100) REVERT: A 117 ASN cc_start: 0.8052 (m-40) cc_final: 0.7732 (m110) REVERT: A 166 GLU cc_start: 0.7352 (tm-30) cc_final: 0.7016 (tm-30) REVERT: A 309 LYS cc_start: 0.7780 (mmtt) cc_final: 0.7526 (mmtt) REVERT: A 329 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7267 (tm-30) REVERT: A 385 TYR cc_start: 0.7948 (p90) cc_final: 0.7600 (p90) REVERT: A 441 LYS cc_start: 0.7872 (tttt) cc_final: 0.7637 (ttpp) REVERT: A 474 MET cc_start: 0.5105 (mmm) cc_final: 0.4767 (mmm) REVERT: A 477 TRP cc_start: 0.7011 (t-100) cc_final: 0.6535 (t-100) REVERT: A 483 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7080 (tp30) REVERT: B 407 VAL cc_start: 0.8743 (t) cc_final: 0.8372 (m) REVERT: B 443 SER cc_start: 0.7872 (m) cc_final: 0.7614 (m) REVERT: B 449 TYR cc_start: 0.7336 (m-80) cc_final: 0.6763 (m-80) REVERT: B 497 PHE cc_start: 0.7246 (m-80) cc_final: 0.6792 (m-80) outliers start: 12 outliers final: 3 residues processed: 200 average time/residue: 0.9153 time to fit residues: 194.7047 Evaluate side-chains 186 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 183 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 446 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 2 optimal weight: 0.0870 chunk 26 optimal weight: 0.2980 chunk 43 optimal weight: 0.0870 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 194 ASN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS A 524 GLN ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.164416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.144995 restraints weight = 15688.283| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.94 r_work: 0.3827 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6729 Z= 0.168 Angle : 0.689 14.465 9166 Z= 0.340 Chirality : 0.046 0.203 979 Planarity : 0.005 0.046 1172 Dihedral : 7.155 57.917 1026 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.87 % Allowed : 18.42 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.30), residues: 790 helix: 1.60 (0.26), residues: 384 sheet: 1.03 (0.73), residues: 45 loop : -0.19 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 610 HIS 0.007 0.001 HIS A 374 PHE 0.020 0.002 PHE B 377 TYR 0.027 0.002 TYR A 385 ARG 0.005 0.001 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 6) link_NAG-ASN : angle 2.51052 ( 18) link_BETA1-4 : bond 0.01552 ( 2) link_BETA1-4 : angle 6.87855 ( 6) hydrogen bonds : bond 0.04732 ( 318) hydrogen bonds : angle 4.63098 ( 925) metal coordination : bond 0.00451 ( 2) SS BOND : bond 0.00212 ( 7) SS BOND : angle 0.49568 ( 14) covalent geometry : bond 0.00372 ( 6712) covalent geometry : angle 0.65764 ( 9128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 63 ASN cc_start: 0.7983 (m-40) cc_final: 0.7666 (m-40) REVERT: A 68 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8148 (ttmm) REVERT: A 69 TRP cc_start: 0.8053 (t-100) cc_final: 0.7757 (t-100) REVERT: A 117 ASN cc_start: 0.8112 (m-40) cc_final: 0.7817 (m110) REVERT: A 166 GLU cc_start: 0.7391 (tm-30) cc_final: 0.6977 (tm-30) REVERT: A 309 LYS cc_start: 0.7811 (mmtt) cc_final: 0.7589 (mmmm) REVERT: A 325 GLN cc_start: 0.7071 (tp40) cc_final: 0.6760 (tp40) REVERT: A 329 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7351 (tm-30) REVERT: A 441 LYS cc_start: 0.7874 (tttt) cc_final: 0.7660 (ttpp) REVERT: A 474 MET cc_start: 0.5030 (mmm) cc_final: 0.4645 (mmt) REVERT: A 478 TRP cc_start: 0.7596 (m100) cc_final: 0.7361 (m100) REVERT: A 489 GLU cc_start: 0.6754 (pm20) cc_final: 0.6521 (pp20) REVERT: A 499 ASP cc_start: 0.7789 (m-30) cc_final: 0.7414 (m-30) REVERT: B 407 VAL cc_start: 0.8786 (t) cc_final: 0.8462 (m) REVERT: B 433 VAL cc_start: 0.7360 (m) cc_final: 0.6945 (p) REVERT: B 449 TYR cc_start: 0.7348 (m-80) cc_final: 0.6742 (m-80) outliers start: 13 outliers final: 2 residues processed: 182 average time/residue: 0.9744 time to fit residues: 188.1455 Evaluate side-chains 167 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 597 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.0980 chunk 45 optimal weight: 0.2980 chunk 36 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 chunk 76 optimal weight: 0.1980 chunk 52 optimal weight: 0.0770 chunk 43 optimal weight: 0.2980 chunk 31 optimal weight: 0.0040 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 0.0670 chunk 55 optimal weight: 0.7980 overall best weight: 0.0888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.165753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.145475 restraints weight = 20555.576| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 3.49 r_work: 0.3814 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3826 r_free = 0.3826 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3826 r_free = 0.3826 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6729 Z= 0.127 Angle : 0.659 14.908 9166 Z= 0.322 Chirality : 0.044 0.186 979 Planarity : 0.005 0.048 1172 Dihedral : 5.999 56.014 1026 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.16 % Allowed : 19.14 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.30), residues: 790 helix: 1.54 (0.26), residues: 398 sheet: 0.99 (0.78), residues: 44 loop : -0.22 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 610 HIS 0.006 0.001 HIS A 374 PHE 0.023 0.001 PHE B 497 TYR 0.022 0.002 TYR A 385 ARG 0.006 0.001 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 6) link_NAG-ASN : angle 2.48920 ( 18) link_BETA1-4 : bond 0.01386 ( 2) link_BETA1-4 : angle 6.75614 ( 6) hydrogen bonds : bond 0.04284 ( 318) hydrogen bonds : angle 4.58781 ( 925) metal coordination : bond 0.00180 ( 2) SS BOND : bond 0.00164 ( 7) SS BOND : angle 0.42805 ( 14) covalent geometry : bond 0.00274 ( 6712) covalent geometry : angle 0.62780 ( 9128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8385 (ttmm) cc_final: 0.8144 (ttmm) REVERT: A 69 TRP cc_start: 0.8056 (t-100) cc_final: 0.7736 (t-100) REVERT: A 166 GLU cc_start: 0.7450 (tm-30) cc_final: 0.6983 (tm-30) REVERT: A 182 GLU cc_start: 0.7349 (tt0) cc_final: 0.6932 (tp30) REVERT: A 325 GLN cc_start: 0.7117 (tp40) cc_final: 0.6789 (tp40) REVERT: A 329 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7503 (tm-30) REVERT: A 366 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7860 (ttp) REVERT: A 441 LYS cc_start: 0.7868 (tttt) cc_final: 0.7657 (ttpp) REVERT: A 453 THR cc_start: 0.8009 (m) cc_final: 0.7637 (p) REVERT: A 474 MET cc_start: 0.5298 (mmm) cc_final: 0.4992 (mmt) REVERT: A 499 ASP cc_start: 0.7857 (m-30) cc_final: 0.7504 (m-30) REVERT: A 522 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8351 (pt0) REVERT: A 559 ARG cc_start: 0.8340 (ppp80) cc_final: 0.8130 (ptt90) REVERT: B 407 VAL cc_start: 0.8751 (t) cc_final: 0.8396 (m) REVERT: B 433 VAL cc_start: 0.7156 (m) cc_final: 0.6822 (p) REVERT: B 443 SER cc_start: 0.7817 (m) cc_final: 0.7532 (m) REVERT: B 449 TYR cc_start: 0.7425 (m-80) cc_final: 0.6828 (m-80) outliers start: 15 outliers final: 4 residues processed: 179 average time/residue: 0.9561 time to fit residues: 182.0188 Evaluate side-chains 181 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 446 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 0.0980 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 0.0770 chunk 19 optimal weight: 0.4980 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 HIS B 343 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.162304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.141372 restraints weight = 25717.774| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 3.87 r_work: 0.3752 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3751 r_free = 0.3751 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3751 r_free = 0.3751 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6729 Z= 0.189 Angle : 0.710 13.745 9166 Z= 0.355 Chirality : 0.046 0.191 979 Planarity : 0.005 0.044 1172 Dihedral : 5.959 58.729 1026 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.45 % Allowed : 21.29 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.30), residues: 790 helix: 1.32 (0.26), residues: 401 sheet: 0.81 (0.74), residues: 43 loop : -0.34 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 610 HIS 0.007 0.002 HIS A 374 PHE 0.021 0.002 PHE B 377 TYR 0.022 0.002 TYR A 50 ARG 0.007 0.001 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 6) link_NAG-ASN : angle 2.52303 ( 18) link_BETA1-4 : bond 0.01398 ( 2) link_BETA1-4 : angle 6.52932 ( 6) hydrogen bonds : bond 0.04825 ( 318) hydrogen bonds : angle 4.64372 ( 925) metal coordination : bond 0.00605 ( 2) SS BOND : bond 0.00218 ( 7) SS BOND : angle 0.50508 ( 14) covalent geometry : bond 0.00429 ( 6712) covalent geometry : angle 0.68162 ( 9128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8223 (ttmm) REVERT: A 69 TRP cc_start: 0.8118 (t-100) cc_final: 0.7910 (t-100) REVERT: A 75 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7844 (mt-10) REVERT: A 131 LYS cc_start: 0.7200 (pttm) cc_final: 0.6755 (pttm) REVERT: A 182 GLU cc_start: 0.7394 (tt0) cc_final: 0.7010 (tp30) REVERT: A 281 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7769 (mt) REVERT: A 291 ILE cc_start: 0.8295 (tp) cc_final: 0.7745 (mt) REVERT: A 329 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7557 (tm-30) REVERT: A 366 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8126 (ttt) REVERT: A 441 LYS cc_start: 0.7976 (tttt) cc_final: 0.7775 (ttpp) REVERT: A 474 MET cc_start: 0.5357 (mmm) cc_final: 0.4713 (mmt) REVERT: A 499 ASP cc_start: 0.7928 (m-30) cc_final: 0.7417 (m-30) REVERT: A 564 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7530 (tm-30) REVERT: B 407 VAL cc_start: 0.8799 (t) cc_final: 0.8441 (m) REVERT: B 433 VAL cc_start: 0.7149 (m) cc_final: 0.6882 (p) REVERT: B 449 TYR cc_start: 0.7488 (m-80) cc_final: 0.6849 (m-80) REVERT: B 462 LYS cc_start: 0.8223 (mmmt) cc_final: 0.7817 (mppt) REVERT: B 465 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6723 (mt-10) outliers start: 17 outliers final: 7 residues processed: 180 average time/residue: 1.0067 time to fit residues: 192.0367 Evaluate side-chains 180 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 171 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 75 optimal weight: 0.3980 chunk 27 optimal weight: 0.0980 chunk 26 optimal weight: 0.0040 chunk 52 optimal weight: 0.1980 chunk 29 optimal weight: 0.0870 chunk 50 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 43 optimal weight: 0.0970 overall best weight: 0.0724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN B 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.165133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.144655 restraints weight = 20760.825| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 3.58 r_work: 0.3811 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6729 Z= 0.129 Angle : 0.688 13.391 9166 Z= 0.340 Chirality : 0.043 0.180 979 Planarity : 0.005 0.041 1172 Dihedral : 5.763 56.035 1026 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.16 % Allowed : 23.17 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.30), residues: 790 helix: 1.55 (0.26), residues: 392 sheet: 0.64 (0.73), residues: 43 loop : -0.40 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.005 0.001 HIS A 374 PHE 0.012 0.001 PHE B 374 TYR 0.023 0.002 TYR A 183 ARG 0.007 0.001 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 6) link_NAG-ASN : angle 2.50250 ( 18) link_BETA1-4 : bond 0.01306 ( 2) link_BETA1-4 : angle 6.37922 ( 6) hydrogen bonds : bond 0.04243 ( 318) hydrogen bonds : angle 4.64921 ( 925) metal coordination : bond 0.00175 ( 2) SS BOND : bond 0.00128 ( 7) SS BOND : angle 0.42993 ( 14) covalent geometry : bond 0.00282 ( 6712) covalent geometry : angle 0.66042 ( 9128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8088 (t-100) cc_final: 0.7866 (t-100) REVERT: A 75 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7705 (mt-10) REVERT: A 94 LYS cc_start: 0.7993 (mtpp) cc_final: 0.7759 (ttpp) REVERT: A 131 LYS cc_start: 0.7214 (pttm) cc_final: 0.6762 (pttm) REVERT: A 281 LEU cc_start: 0.7929 (tt) cc_final: 0.7718 (mt) REVERT: A 329 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7548 (tm-30) REVERT: A 366 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7749 (ttp) REVERT: A 441 LYS cc_start: 0.7900 (tttt) cc_final: 0.7694 (ttpp) REVERT: A 474 MET cc_start: 0.5364 (mmm) cc_final: 0.4903 (mmm) REVERT: A 482 ARG cc_start: 0.8027 (mtt90) cc_final: 0.7817 (mtt180) REVERT: A 600 LYS cc_start: 0.7330 (ptmm) cc_final: 0.6940 (ptmm) REVERT: B 399 SER cc_start: 0.7529 (p) cc_final: 0.7264 (m) REVERT: B 407 VAL cc_start: 0.8784 (t) cc_final: 0.8428 (m) REVERT: B 433 VAL cc_start: 0.7095 (m) cc_final: 0.6871 (p) REVERT: B 443 SER cc_start: 0.7781 (m) cc_final: 0.7483 (m) REVERT: B 449 TYR cc_start: 0.7466 (m-80) cc_final: 0.6806 (m-80) REVERT: B 462 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7660 (mppt) outliers start: 15 outliers final: 8 residues processed: 181 average time/residue: 0.9481 time to fit residues: 181.8280 Evaluate side-chains 180 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 171 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 442 GLN A 556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.160393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.141374 restraints weight = 15000.578| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.89 r_work: 0.3785 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 6729 Z= 0.252 Angle : 0.789 12.711 9166 Z= 0.401 Chirality : 0.050 0.207 979 Planarity : 0.005 0.043 1172 Dihedral : 6.433 59.886 1026 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.88 % Allowed : 24.03 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.29), residues: 790 helix: 1.12 (0.25), residues: 402 sheet: 0.67 (0.72), residues: 42 loop : -0.62 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 477 HIS 0.008 0.002 HIS A 374 PHE 0.022 0.003 PHE A 512 TYR 0.027 0.003 TYR A 183 ARG 0.006 0.001 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 6) link_NAG-ASN : angle 2.79822 ( 18) link_BETA1-4 : bond 0.01098 ( 2) link_BETA1-4 : angle 6.33678 ( 6) hydrogen bonds : bond 0.05425 ( 318) hydrogen bonds : angle 4.76353 ( 925) metal coordination : bond 0.00796 ( 2) SS BOND : bond 0.00267 ( 7) SS BOND : angle 0.56810 ( 14) covalent geometry : bond 0.00575 ( 6712) covalent geometry : angle 0.76366 ( 9128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LYS cc_start: 0.7180 (pttm) cc_final: 0.6799 (pttm) REVERT: A 329 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7483 (tm-30) REVERT: A 366 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8061 (ttt) REVERT: A 385 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7968 (p90) REVERT: A 559 ARG cc_start: 0.8319 (ppp80) cc_final: 0.8094 (ptt90) REVERT: A 564 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7273 (tm-30) REVERT: A 571 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6730 (tm-30) REVERT: B 407 VAL cc_start: 0.8806 (t) cc_final: 0.8512 (m) REVERT: B 449 TYR cc_start: 0.7446 (m-80) cc_final: 0.7036 (m-80) outliers start: 20 outliers final: 7 residues processed: 186 average time/residue: 0.9518 time to fit residues: 187.8954 Evaluate side-chains 184 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 446 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 29 optimal weight: 0.0970 chunk 22 optimal weight: 0.0970 chunk 58 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 overall best weight: 0.1174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 64 ASN B 505 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.162962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.142844 restraints weight = 18596.399| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 3.33 r_work: 0.3794 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6729 Z= 0.145 Angle : 0.756 12.700 9166 Z= 0.375 Chirality : 0.045 0.189 979 Planarity : 0.005 0.040 1172 Dihedral : 6.102 56.025 1026 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.45 % Allowed : 24.46 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 790 helix: 1.27 (0.26), residues: 400 sheet: 0.63 (0.74), residues: 42 loop : -0.58 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 168 HIS 0.005 0.001 HIS A 374 PHE 0.024 0.001 PHE B 497 TYR 0.021 0.002 TYR A 385 ARG 0.008 0.001 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 6) link_NAG-ASN : angle 2.58917 ( 18) link_BETA1-4 : bond 0.01257 ( 2) link_BETA1-4 : angle 6.21437 ( 6) hydrogen bonds : bond 0.04628 ( 318) hydrogen bonds : angle 4.76449 ( 925) metal coordination : bond 0.00142 ( 2) SS BOND : bond 0.00138 ( 7) SS BOND : angle 0.45932 ( 14) covalent geometry : bond 0.00327 ( 6712) covalent geometry : angle 0.73132 ( 9128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7855 (ttpp) REVERT: A 131 LYS cc_start: 0.7133 (pttm) cc_final: 0.6793 (pttm) REVERT: A 329 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 366 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7888 (ttt) REVERT: A 385 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7942 (p90) REVERT: A 414 THR cc_start: 0.8019 (t) cc_final: 0.7738 (m) REVERT: A 455 MET cc_start: 0.7853 (tmm) cc_final: 0.7286 (tmm) REVERT: A 522 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8257 (pt0) REVERT: A 564 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7191 (tm-30) REVERT: B 407 VAL cc_start: 0.8778 (t) cc_final: 0.8458 (m) REVERT: B 449 TYR cc_start: 0.7365 (m-80) cc_final: 0.6891 (m-80) REVERT: B 457 ARG cc_start: 0.7390 (tmm-80) cc_final: 0.6134 (ttp80) outliers start: 17 outliers final: 9 residues processed: 173 average time/residue: 1.0310 time to fit residues: 188.8805 Evaluate side-chains 176 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 446 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 0.0980 chunk 42 optimal weight: 0.0870 chunk 68 optimal weight: 0.0870 chunk 70 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 chunk 75 optimal weight: 0.0770 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 overall best weight: 0.0894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.163812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.144278 restraints weight = 17354.974| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 3.18 r_work: 0.3826 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3828 r_free = 0.3828 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6729 Z= 0.140 Angle : 0.747 12.374 9166 Z= 0.375 Chirality : 0.045 0.200 979 Planarity : 0.005 0.039 1172 Dihedral : 5.918 57.147 1026 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.01 % Allowed : 25.90 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.30), residues: 790 helix: 1.24 (0.26), residues: 395 sheet: 0.59 (0.72), residues: 42 loop : -0.43 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 168 HIS 0.006 0.001 HIS A 374 PHE 0.016 0.001 PHE B 497 TYR 0.026 0.002 TYR A 50 ARG 0.007 0.001 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 6) link_NAG-ASN : angle 2.32604 ( 18) link_BETA1-4 : bond 0.01207 ( 2) link_BETA1-4 : angle 6.09338 ( 6) hydrogen bonds : bond 0.04403 ( 318) hydrogen bonds : angle 4.74720 ( 925) metal coordination : bond 0.00132 ( 2) SS BOND : bond 0.00118 ( 7) SS BOND : angle 0.39564 ( 14) covalent geometry : bond 0.00317 ( 6712) covalent geometry : angle 0.72503 ( 9128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8065 (mtpp) cc_final: 0.7830 (ttpp) REVERT: A 131 LYS cc_start: 0.7028 (pttm) cc_final: 0.6662 (pttm) REVERT: A 208 GLU cc_start: 0.7762 (tt0) cc_final: 0.7505 (tt0) REVERT: A 329 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7544 (tm-30) REVERT: A 385 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7881 (p90) REVERT: A 414 THR cc_start: 0.8012 (t) cc_final: 0.7726 (m) REVERT: A 455 MET cc_start: 0.7814 (tmm) cc_final: 0.7274 (tmm) REVERT: A 522 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8279 (pt0) REVERT: A 564 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7132 (tm-30) REVERT: A 595 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7774 (mp) REVERT: A 600 LYS cc_start: 0.7403 (ptmm) cc_final: 0.7017 (ptmm) REVERT: B 407 VAL cc_start: 0.8734 (t) cc_final: 0.8423 (m) REVERT: B 449 TYR cc_start: 0.7415 (m-80) cc_final: 0.6951 (m-80) outliers start: 14 outliers final: 8 residues processed: 172 average time/residue: 1.0692 time to fit residues: 194.1850 Evaluate side-chains 170 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 437 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.0570 chunk 77 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 53 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 overall best weight: 0.1614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.163819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.143625 restraints weight = 20675.162| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 3.54 r_work: 0.3797 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3800 r_free = 0.3800 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3800 r_free = 0.3800 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 6729 Z= 0.223 Angle : 1.075 59.182 9166 Z= 0.616 Chirality : 0.048 0.415 979 Planarity : 0.006 0.086 1172 Dihedral : 5.931 57.167 1026 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.87 % Allowed : 26.91 % Favored : 71.22 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.30), residues: 790 helix: 1.23 (0.26), residues: 395 sheet: 0.35 (0.73), residues: 42 loop : -0.42 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 168 HIS 0.006 0.001 HIS A 374 PHE 0.016 0.001 PHE B 497 TYR 0.034 0.002 TYR A 613 ARG 0.008 0.001 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 6) link_NAG-ASN : angle 2.31834 ( 18) link_BETA1-4 : bond 0.01177 ( 2) link_BETA1-4 : angle 6.11372 ( 6) hydrogen bonds : bond 0.04443 ( 318) hydrogen bonds : angle 4.74884 ( 925) metal coordination : bond 0.00224 ( 2) SS BOND : bond 0.00125 ( 7) SS BOND : angle 0.39878 ( 14) covalent geometry : bond 0.00474 ( 6712) covalent geometry : angle 1.06078 ( 9128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8067 (mtpp) cc_final: 0.7834 (ttpp) REVERT: A 131 LYS cc_start: 0.7053 (pttm) cc_final: 0.6688 (pttm) REVERT: A 208 GLU cc_start: 0.7788 (tt0) cc_final: 0.7546 (tt0) REVERT: A 329 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7605 (tm-30) REVERT: A 385 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7886 (p90) REVERT: A 414 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7710 (m) REVERT: A 455 MET cc_start: 0.7837 (tmm) cc_final: 0.7307 (tmm) REVERT: A 474 MET cc_start: 0.5297 (mmt) cc_final: 0.4721 (mmt) REVERT: A 522 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8272 (pt0) REVERT: A 595 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7778 (mp) REVERT: A 600 LYS cc_start: 0.7412 (ptmm) cc_final: 0.7036 (ptmm) REVERT: B 407 VAL cc_start: 0.8741 (t) cc_final: 0.8442 (m) REVERT: B 449 TYR cc_start: 0.7443 (m-80) cc_final: 0.6972 (m-80) outliers start: 13 outliers final: 9 residues processed: 164 average time/residue: 0.9845 time to fit residues: 171.4558 Evaluate side-chains 170 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.0870 chunk 36 optimal weight: 0.3980 chunk 50 optimal weight: 0.0670 chunk 68 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 0.0970 chunk 72 optimal weight: 0.0770 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 overall best weight: 0.1452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.163765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.143431 restraints weight = 20974.844| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 3.59 r_work: 0.3798 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 6729 Z= 0.223 Angle : 1.075 59.182 9166 Z= 0.616 Chirality : 0.048 0.415 979 Planarity : 0.006 0.086 1172 Dihedral : 5.931 57.167 1026 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.87 % Allowed : 26.91 % Favored : 71.22 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.30), residues: 790 helix: 1.23 (0.26), residues: 395 sheet: 0.35 (0.73), residues: 42 loop : -0.42 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 168 HIS 0.006 0.001 HIS A 374 PHE 0.016 0.001 PHE B 497 TYR 0.034 0.002 TYR A 613 ARG 0.008 0.001 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 6) link_NAG-ASN : angle 2.31834 ( 18) link_BETA1-4 : bond 0.01177 ( 2) link_BETA1-4 : angle 6.11372 ( 6) hydrogen bonds : bond 0.04443 ( 318) hydrogen bonds : angle 4.74884 ( 925) metal coordination : bond 0.00224 ( 2) SS BOND : bond 0.00125 ( 7) SS BOND : angle 0.39878 ( 14) covalent geometry : bond 0.00474 ( 6712) covalent geometry : angle 1.06078 ( 9128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6162.98 seconds wall clock time: 106 minutes 51.23 seconds (6411.23 seconds total)