Starting phenix.real_space_refine on Tue Jun 10 11:25:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8we1_37470/06_2025/8we1_37470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8we1_37470/06_2025/8we1_37470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8we1_37470/06_2025/8we1_37470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8we1_37470/06_2025/8we1_37470.map" model { file = "/net/cci-nas-00/data/ceres_data/8we1_37470/06_2025/8we1_37470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8we1_37470/06_2025/8we1_37470.cif" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 6332 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 4194 2.51 5 N 1077 2.21 5 O 1250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6559 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4872 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4987 Chain: "B" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1550 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "C" 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 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: 6.54, per 1000 atoms: 1.00 Number of scatterers: 6559 At special positions: 0 Unit cell: (74.8, 87.55, 124.95, 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 1250 8.00 N 1077 7.00 C 4194 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 D 1 " - " NAG D 2 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 901 " - " ASN A 53 " " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 322 " " NAG A 904 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 103 " " NAG D 1 " - " ASN A 546 " Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 905 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 374 " 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: 1492 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 53.1% alpha, 5.6% 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: 4.510A pdb=" N ASP A 38 " --> pdb=" O AHIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.784A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 4.072A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.831A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.554A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.608A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) 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 249 removed outlier: 3.837A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (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 299 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.947A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.594A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.935A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.679A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.275A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.532A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.611A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.685A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.773A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.793A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.299A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.101A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.725A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 289 hydrogen bonds defined for protein. 820 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: 1.62 Time building geometry restraints manager: 2.20 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: 2079 1.34 - 1.46: 1687 1.46 - 1.58: 2920 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6744 Sorted by residual: bond pdb=" CE1BHIS A 34 " pdb=" NE2BHIS A 34 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.55e+01 bond pdb=" CE1AHIS A 34 " pdb=" NE2AHIS A 34 " ideal model delta sigma weight residual 1.321 1.358 -0.037 1.00e-02 1.00e+04 1.36e+01 bond pdb=" N GLN A 24 " pdb=" CA GLN A 24 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.21e-02 6.83e+03 9.89e+00 bond pdb=" N ASN B 477 " pdb=" CA ASN B 477 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.16e-02 7.43e+03 7.75e+00 bond pdb=" N GLN B 493 " pdb=" CA GLN B 493 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.85e+00 ... (remaining 6739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 9038 2.32 - 4.64: 116 4.64 - 6.97: 16 6.97 - 9.29: 0 9.29 - 11.61: 1 Bond angle restraints: 9171 Sorted by residual: angle pdb=" C TYR A 83 " pdb=" N PRO A 84 " pdb=" CA PRO A 84 " ideal model delta sigma weight residual 119.78 123.81 -4.03 1.03e+00 9.43e-01 1.53e+01 angle pdb=" CB MET A 408 " pdb=" CG MET A 408 " pdb=" SD MET A 408 " ideal model delta sigma weight residual 112.70 124.31 -11.61 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CA AHIS A 34 " pdb=" C AHIS A 34 " pdb=" O AHIS A 34 " ideal model delta sigma weight residual 119.97 116.07 3.90 1.15e+00 7.56e-01 1.15e+01 angle pdb=" CA GLU A 150 " pdb=" CB GLU A 150 " pdb=" CG GLU A 150 " ideal model delta sigma weight residual 114.10 120.47 -6.37 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C ASN B 487 " pdb=" CA ASN B 487 " pdb=" CB ASN B 487 " ideal model delta sigma weight residual 111.51 116.17 -4.66 1.58e+00 4.01e-01 8.69e+00 ... (remaining 9166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 3590 21.39 - 42.78: 399 42.78 - 64.16: 90 64.16 - 85.55: 17 85.55 - 106.94: 7 Dihedral angle restraints: 4103 sinusoidal: 1777 harmonic: 2326 Sorted by residual: dihedral pdb=" CA GLN A 139 " pdb=" C GLN A 139 " pdb=" N GLU A 140 " pdb=" CA GLU A 140 " ideal model delta harmonic sigma weight residual 180.00 153.86 26.14 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" C2 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C4 NAG A 901 " pdb=" C5 NAG A 901 " ideal model delta sinusoidal sigma weight residual 53.78 -53.16 106.94 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C2 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C4 NAG A 901 " pdb=" O4 NAG A 901 " ideal model delta sinusoidal sigma weight residual 175.11 68.48 106.63 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 4100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 843 0.059 - 0.118: 130 0.118 - 0.178: 12 0.178 - 0.237: 1 0.237 - 0.296: 1 Chirality restraints: 987 Sorted by residual: chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 53 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ASN B 477 " pdb=" N ASN B 477 " pdb=" C ASN B 477 " pdb=" CB ASN B 477 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 984 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA AHIS A 34 " 0.028 2.00e-02 2.50e+03 5.63e-02 3.17e+01 pdb=" C AHIS A 34 " -0.097 2.00e-02 2.50e+03 pdb=" O AHIS A 34 " 0.036 2.00e-02 2.50e+03 pdb=" N GLU A 35 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 414 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO A 415 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA BHIS A 34 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C BHIS A 34 " 0.036 2.00e-02 2.50e+03 pdb=" O BHIS A 34 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 35 " -0.013 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 52 2.58 - 3.16: 5107 3.16 - 3.74: 10141 3.74 - 4.32: 13701 4.32 - 4.90: 23083 Nonbonded interactions: 52084 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 905 " model vdw 2.001 2.230 nonbonded pdb=" OD1 ASP A 494 " pdb=" OG1 THR A 496 " model vdw 2.164 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.165 3.040 nonbonded pdb=" OG SER A 109 " pdb=" OD1 ASP A 111 " model vdw 2.177 3.040 nonbonded pdb=" O ALA A 501 " pdb=" OG SER A 507 " model vdw 2.188 3.040 ... (remaining 52079 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.690 Find NCS groups from input model: 0.070 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 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 0.199 6763 Z= 0.230 Angle : 0.619 11.611 9215 Z= 0.326 Chirality : 0.044 0.296 987 Planarity : 0.004 0.059 1177 Dihedral : 18.672 106.937 2590 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.89 % Allowed : 25.36 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.31), residues: 790 helix: 1.60 (0.28), residues: 370 sheet: 0.79 (0.76), residues: 45 loop : -0.79 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 203 HIS 0.005 0.001 HIS A 241 PHE 0.011 0.001 PHE B 347 TYR 0.025 0.001 TYR A 521 ARG 0.006 0.001 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00593 ( 7) link_NAG-ASN : angle 2.38613 ( 21) link_BETA1-4 : bond 0.00410 ( 2) link_BETA1-4 : angle 0.84185 ( 6) hydrogen bonds : bond 0.17674 ( 289) hydrogen bonds : angle 5.35209 ( 820) link_BETA1-6 : bond 0.00400 ( 1) link_BETA1-6 : angle 1.55128 ( 3) metal coordination : bond 0.19891 ( 2) SS BOND : bond 0.00246 ( 7) SS BOND : angle 0.48696 ( 14) covalent geometry : bond 0.00366 ( 6744) covalent geometry : angle 0.60881 ( 9171) *********************** 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 191 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.707 Fit side-chains REVERT: B 364 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6739 (p0) outliers start: 27 outliers final: 23 residues processed: 186 average time/residue: 1.0388 time to fit residues: 204.0646 Evaluate side-chains 178 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 61 ASN A 81 GLN A 154 ASN A 210 ASN A 374 HIS A 580 ASN A 586 ASN B 439 ASN B 448 ASN B 450 ASN B 487 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.138892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.119198 restraints weight = 18028.457| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.88 r_work: 0.3521 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.556 6763 Z= 0.267 Angle : 0.586 12.454 9215 Z= 0.287 Chirality : 0.044 0.251 987 Planarity : 0.004 0.058 1177 Dihedral : 10.554 76.217 1118 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.19 % Allowed : 22.33 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.62 (0.30), residues: 790 helix: 1.60 (0.28), residues: 370 sheet: 0.51 (0.74), residues: 45 loop : -0.82 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 203 HIS 0.006 0.001 HIS A 241 PHE 0.008 0.001 PHE B 347 TYR 0.021 0.001 TYR A 521 ARG 0.004 0.001 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00707 ( 7) link_NAG-ASN : angle 2.73169 ( 21) link_BETA1-4 : bond 0.00304 ( 2) link_BETA1-4 : angle 0.86384 ( 6) hydrogen bonds : bond 0.05073 ( 289) hydrogen bonds : angle 4.24691 ( 820) link_BETA1-6 : bond 0.00390 ( 1) link_BETA1-6 : angle 1.43417 ( 3) metal coordination : bond 0.39307 ( 2) SS BOND : bond 0.00375 ( 7) SS BOND : angle 0.55407 ( 14) covalent geometry : bond 0.00319 ( 6744) covalent geometry : angle 0.57174 ( 9171) *********************** 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 200 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.677 Fit side-chains REVERT: A 364 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8153 (t) REVERT: B 364 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7422 (p0) outliers start: 36 outliers final: 27 residues processed: 182 average time/residue: 1.0302 time to fit residues: 198.2806 Evaluate side-chains 179 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 0.0000 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 340 GLN A 580 ASN A 586 ASN B 370 ASN B 448 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.138960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.121127 restraints weight = 10975.711| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.21 r_work: 0.3573 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6763 Z= 0.137 Angle : 0.571 11.503 9215 Z= 0.277 Chirality : 0.044 0.323 987 Planarity : 0.004 0.059 1177 Dihedral : 7.270 58.085 1095 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.48 % Allowed : 22.77 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.59 (0.30), residues: 790 helix: 1.60 (0.27), residues: 370 sheet: 0.30 (0.73), residues: 45 loop : -0.84 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 203 HIS 0.006 0.001 HIS A 241 PHE 0.010 0.001 PHE B 347 TYR 0.018 0.001 TYR A 521 ARG 0.005 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00656 ( 7) link_NAG-ASN : angle 2.76931 ( 21) link_BETA1-4 : bond 0.00400 ( 2) link_BETA1-4 : angle 0.85464 ( 6) hydrogen bonds : bond 0.04731 ( 289) hydrogen bonds : angle 4.00012 ( 820) link_BETA1-6 : bond 0.00286 ( 1) link_BETA1-6 : angle 1.32834 ( 3) metal coordination : bond 0.00650 ( 2) SS BOND : bond 0.00336 ( 7) SS BOND : angle 0.50216 ( 14) covalent geometry : bond 0.00310 ( 6744) covalent geometry : angle 0.55595 ( 9171) *********************** 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 193 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.685 Fit side-chains REVERT: A 364 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8187 (t) REVERT: B 423 TYR cc_start: 0.8047 (t80) cc_final: 0.7845 (t80) outliers start: 38 outliers final: 26 residues processed: 171 average time/residue: 1.1376 time to fit residues: 204.8706 Evaluate side-chains 175 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 68 optimal weight: 0.0570 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 188 ASN A 194 ASN A 580 ASN A 586 ASN B 354 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.138292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.117848 restraints weight = 21336.610| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.21 r_work: 0.3490 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6763 Z= 0.145 Angle : 0.566 11.588 9215 Z= 0.278 Chirality : 0.044 0.308 987 Planarity : 0.004 0.059 1177 Dihedral : 6.470 54.458 1088 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.19 % Allowed : 23.63 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.57 (0.30), residues: 790 helix: 1.60 (0.27), residues: 370 sheet: 0.43 (0.72), residues: 45 loop : -0.89 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 168 HIS 0.007 0.001 HIS A 241 PHE 0.008 0.001 PHE A 72 TYR 0.019 0.001 TYR A 521 ARG 0.006 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00630 ( 7) link_NAG-ASN : angle 2.76960 ( 21) link_BETA1-4 : bond 0.00365 ( 2) link_BETA1-4 : angle 0.86341 ( 6) hydrogen bonds : bond 0.04744 ( 289) hydrogen bonds : angle 3.96489 ( 820) link_BETA1-6 : bond 0.00255 ( 1) link_BETA1-6 : angle 1.41512 ( 3) metal coordination : bond 0.00244 ( 2) SS BOND : bond 0.00331 ( 7) SS BOND : angle 0.47417 ( 14) covalent geometry : bond 0.00333 ( 6744) covalent geometry : angle 0.55020 ( 9171) *********************** 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 197 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.686 Fit side-chains REVERT: A 364 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8198 (t) REVERT: B 386 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7563 (tmmm) outliers start: 36 outliers final: 24 residues processed: 174 average time/residue: 1.0428 time to fit residues: 191.3556 Evaluate side-chains 177 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 30 optimal weight: 0.0970 chunk 77 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 188 ASN A 194 ASN A 580 ASN A 586 ASN B 354 ASN B 448 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.137752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.120768 restraints weight = 8922.633| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.95 r_work: 0.3586 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6763 Z= 0.150 Angle : 0.576 12.246 9215 Z= 0.281 Chirality : 0.044 0.310 987 Planarity : 0.004 0.059 1177 Dihedral : 6.229 54.535 1087 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.91 % Allowed : 22.62 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.46 (0.30), residues: 790 helix: 1.49 (0.27), residues: 376 sheet: 0.57 (0.73), residues: 45 loop : -1.00 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 168 HIS 0.007 0.001 HIS A 241 PHE 0.008 0.001 PHE A 72 TYR 0.020 0.001 TYR A 521 ARG 0.009 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 7) link_NAG-ASN : angle 2.74158 ( 21) link_BETA1-4 : bond 0.00357 ( 2) link_BETA1-4 : angle 0.87996 ( 6) hydrogen bonds : bond 0.04810 ( 289) hydrogen bonds : angle 3.94219 ( 820) link_BETA1-6 : bond 0.00229 ( 1) link_BETA1-6 : angle 1.43379 ( 3) metal coordination : bond 0.00229 ( 2) SS BOND : bond 0.00345 ( 7) SS BOND : angle 0.48627 ( 14) covalent geometry : bond 0.00348 ( 6744) covalent geometry : angle 0.56055 ( 9171) *********************** 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 198 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.673 Fit side-chains REVERT: A 197 GLU cc_start: 0.7210 (pm20) cc_final: 0.6971 (mp0) REVERT: A 364 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8214 (t) REVERT: B 386 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7202 (tmmm) outliers start: 41 outliers final: 31 residues processed: 174 average time/residue: 1.0538 time to fit residues: 193.4549 Evaluate side-chains 185 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 0.0870 chunk 59 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 194 ASN A 580 ASN A 586 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.138445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.118944 restraints weight = 16467.880| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.78 r_work: 0.3525 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6763 Z= 0.134 Angle : 0.569 12.136 9215 Z= 0.277 Chirality : 0.044 0.303 987 Planarity : 0.004 0.058 1177 Dihedral : 6.089 53.959 1087 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.48 % Allowed : 23.49 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.45 (0.30), residues: 790 helix: 1.49 (0.27), residues: 376 sheet: 0.59 (0.74), residues: 45 loop : -1.02 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 168 HIS 0.006 0.001 HIS A 241 PHE 0.008 0.001 PHE B 456 TYR 0.018 0.001 TYR A 521 ARG 0.007 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00620 ( 7) link_NAG-ASN : angle 2.66072 ( 21) link_BETA1-4 : bond 0.00372 ( 2) link_BETA1-4 : angle 0.90949 ( 6) hydrogen bonds : bond 0.04582 ( 289) hydrogen bonds : angle 3.90688 ( 820) link_BETA1-6 : bond 0.00233 ( 1) link_BETA1-6 : angle 1.42439 ( 3) metal coordination : bond 0.00166 ( 2) SS BOND : bond 0.00303 ( 7) SS BOND : angle 0.46306 ( 14) covalent geometry : bond 0.00307 ( 6744) covalent geometry : angle 0.55482 ( 9171) *********************** 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 197 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.660 Fit side-chains REVERT: A 197 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: B 386 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7180 (tmmm) outliers start: 38 outliers final: 27 residues processed: 173 average time/residue: 1.0144 time to fit residues: 185.6765 Evaluate side-chains 183 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 194 ASN A 586 ASN B 354 ASN B 448 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.138428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.121450 restraints weight = 8765.477| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.94 r_work: 0.3595 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6763 Z= 0.134 Angle : 0.575 12.493 9215 Z= 0.279 Chirality : 0.044 0.302 987 Planarity : 0.004 0.057 1177 Dihedral : 5.757 53.819 1083 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.90 % Allowed : 23.78 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.47 (0.30), residues: 790 helix: 1.51 (0.27), residues: 376 sheet: 0.63 (0.74), residues: 45 loop : -1.02 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 69 HIS 0.006 0.001 HIS A 241 PHE 0.008 0.001 PHE A 72 TYR 0.020 0.001 TYR A 521 ARG 0.008 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 7) link_NAG-ASN : angle 2.60677 ( 21) link_BETA1-4 : bond 0.00375 ( 2) link_BETA1-4 : angle 0.92641 ( 6) hydrogen bonds : bond 0.04550 ( 289) hydrogen bonds : angle 3.90271 ( 820) link_BETA1-6 : bond 0.00243 ( 1) link_BETA1-6 : angle 1.43591 ( 3) metal coordination : bond 0.00106 ( 2) SS BOND : bond 0.00307 ( 7) SS BOND : angle 0.48762 ( 14) covalent geometry : bond 0.00307 ( 6744) covalent geometry : angle 0.56099 ( 9171) *********************** 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 194 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 0.723 Fit side-chains REVERT: A 197 GLU cc_start: 0.7219 (pm20) cc_final: 0.6968 (mp0) outliers start: 34 outliers final: 29 residues processed: 174 average time/residue: 1.0090 time to fit residues: 185.7002 Evaluate side-chains 182 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 0.0870 chunk 53 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 chunk 40 optimal weight: 0.9980 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 194 ASN A 586 ASN B 422 ASN B 448 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.140251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.120827 restraints weight = 16567.001| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.80 r_work: 0.3551 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6763 Z= 0.104 Angle : 0.549 12.624 9215 Z= 0.265 Chirality : 0.042 0.279 987 Planarity : 0.004 0.055 1177 Dihedral : 5.383 52.559 1077 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.75 % Allowed : 25.94 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.59 (0.30), residues: 790 helix: 1.61 (0.27), residues: 376 sheet: 0.59 (0.74), residues: 45 loop : -0.94 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 168 HIS 0.004 0.001 HIS A 241 PHE 0.009 0.001 PHE B 456 TYR 0.018 0.001 TYR A 521 ARG 0.007 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00568 ( 7) link_NAG-ASN : angle 2.43121 ( 21) link_BETA1-4 : bond 0.00418 ( 2) link_BETA1-4 : angle 0.91615 ( 6) hydrogen bonds : bond 0.03910 ( 289) hydrogen bonds : angle 3.80042 ( 820) link_BETA1-6 : bond 0.00315 ( 1) link_BETA1-6 : angle 1.36257 ( 3) metal coordination : bond 0.00127 ( 2) SS BOND : bond 0.00229 ( 7) SS BOND : angle 0.46101 ( 14) covalent geometry : bond 0.00227 ( 6744) covalent geometry : angle 0.53699 ( 9171) *********************** 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 183 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.707 Fit side-chains REVERT: A 197 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6763 (mp0) outliers start: 26 outliers final: 21 residues processed: 168 average time/residue: 0.9487 time to fit residues: 168.9994 Evaluate side-chains 173 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 194 ASN A 210 ASN A 586 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.137598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.118160 restraints weight = 17278.762| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.80 r_work: 0.3514 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6763 Z= 0.185 Angle : 0.636 12.667 9215 Z= 0.311 Chirality : 0.046 0.310 987 Planarity : 0.004 0.056 1177 Dihedral : 5.628 54.339 1077 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.89 % Allowed : 25.22 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.30), residues: 790 helix: 1.50 (0.27), residues: 376 sheet: 0.59 (0.73), residues: 45 loop : -1.13 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 168 HIS 0.008 0.001 HIS A 241 PHE 0.009 0.001 PHE A 308 TYR 0.025 0.002 TYR A 521 ARG 0.008 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 7) link_NAG-ASN : angle 2.64877 ( 21) link_BETA1-4 : bond 0.00526 ( 2) link_BETA1-4 : angle 1.03880 ( 6) hydrogen bonds : bond 0.05016 ( 289) hydrogen bonds : angle 3.91741 ( 820) link_BETA1-6 : bond 0.00377 ( 1) link_BETA1-6 : angle 1.54358 ( 3) metal coordination : bond 0.00187 ( 2) SS BOND : bond 0.00382 ( 7) SS BOND : angle 1.91351 ( 14) covalent geometry : bond 0.00433 ( 6744) covalent geometry : angle 0.61878 ( 9171) *********************** 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 185 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.691 Fit side-chains REVERT: A 197 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6846 (mp0) outliers start: 27 outliers final: 24 residues processed: 169 average time/residue: 1.0472 time to fit residues: 187.0973 Evaluate side-chains 180 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 61 optimal weight: 0.2980 chunk 54 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 194 ASN A 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.137800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.120010 restraints weight = 11257.349| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.21 r_work: 0.3564 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6763 Z= 0.168 Angle : 0.621 12.692 9215 Z= 0.302 Chirality : 0.046 0.314 987 Planarity : 0.004 0.058 1177 Dihedral : 5.642 54.212 1077 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.75 % Allowed : 25.22 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.30), residues: 790 helix: 1.37 (0.27), residues: 382 sheet: 0.57 (0.72), residues: 45 loop : -1.12 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 203 HIS 0.007 0.001 HIS A 241 PHE 0.010 0.001 PHE B 347 TYR 0.023 0.002 TYR A 521 ARG 0.008 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 7) link_NAG-ASN : angle 2.67598 ( 21) link_BETA1-4 : bond 0.00356 ( 2) link_BETA1-4 : angle 1.00235 ( 6) hydrogen bonds : bond 0.04904 ( 289) hydrogen bonds : angle 3.95613 ( 820) link_BETA1-6 : bond 0.00224 ( 1) link_BETA1-6 : angle 1.49859 ( 3) metal coordination : bond 0.00249 ( 2) SS BOND : bond 0.00356 ( 7) SS BOND : angle 1.76937 ( 14) covalent geometry : bond 0.00394 ( 6744) covalent geometry : angle 0.60384 ( 9171) ********************** 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 182 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.648 Fit side-chains REVERT: A 197 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: A 364 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8231 (t) REVERT: B 424 LYS cc_start: 0.8125 (tppt) cc_final: 0.7782 (tppt) outliers start: 26 outliers final: 19 residues processed: 166 average time/residue: 1.0762 time to fit residues: 188.4482 Evaluate side-chains 176 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 194 ASN A 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.138526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.119156 restraints weight = 16356.139| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.75 r_work: 0.3530 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6763 Z= 0.141 Angle : 0.601 12.806 9215 Z= 0.292 Chirality : 0.044 0.305 987 Planarity : 0.004 0.057 1177 Dihedral : 5.564 53.447 1077 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.03 % Allowed : 26.37 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.36 (0.30), residues: 790 helix: 1.47 (0.27), residues: 376 sheet: 0.56 (0.73), residues: 45 loop : -1.14 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 203 HIS 0.006 0.001 HIS A 241 PHE 0.008 0.001 PHE A 72 TYR 0.023 0.001 TYR A 521 ARG 0.008 0.001 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 7) link_NAG-ASN : angle 2.58135 ( 21) link_BETA1-4 : bond 0.00381 ( 2) link_BETA1-4 : angle 0.97125 ( 6) hydrogen bonds : bond 0.04604 ( 289) hydrogen bonds : angle 3.91244 ( 820) link_BETA1-6 : bond 0.00216 ( 1) link_BETA1-6 : angle 1.47774 ( 3) metal coordination : bond 0.00186 ( 2) SS BOND : bond 0.00301 ( 7) SS BOND : angle 1.22939 ( 14) covalent geometry : bond 0.00325 ( 6744) covalent geometry : angle 0.58700 ( 9171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6911.88 seconds wall clock time: 118 minutes 11.69 seconds (7091.69 seconds total)