Starting phenix.real_space_refine on Sat Aug 23 10:56:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8we1_37470/08_2025/8we1_37470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8we1_37470/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8we1_37470/08_2025/8we1_37470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8we1_37470/08_2025/8we1_37470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8we1_37470/08_2025/8we1_37470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8we1_37470/08_2025/8we1_37470.map" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.47, per 1000 atoms: 0.38 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: 0.49 Conformation dependent library (CDL) restraints added in 505.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.21 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: 1.08 Time building geometry restraints manager: 0.66 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.670 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.000 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (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 ARG 0.006 0.001 ARG B 454 TYR 0.025 0.001 TYR A 521 PHE 0.011 0.001 PHE B 347 TRP 0.009 0.001 TRP A 203 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6744) covalent geometry : angle 0.60881 ( 9171) SS BOND : bond 0.00246 ( 7) SS BOND : angle 0.48696 ( 14) hydrogen bonds : bond 0.17674 ( 289) hydrogen bonds : angle 5.35209 ( 820) metal coordination : bond 0.19891 ( 2) link_BETA1-4 : bond 0.00410 ( 2) link_BETA1-4 : angle 0.84185 ( 6) link_BETA1-6 : bond 0.00400 ( 1) link_BETA1-6 : angle 1.55128 ( 3) link_NAG-ASN : bond 0.00593 ( 7) link_NAG-ASN : angle 2.38613 ( 21) *********************** 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 : 0.284 Fit side-chains outliers start: 27 outliers final: 23 residues processed: 186 average time/residue: 0.5211 time to fit residues: 102.0799 Evaluate side-chains 177 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 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 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.139173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.119462 restraints weight = 17911.260| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.87 r_work: 0.3525 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 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 = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.555 6763 Z= 0.262 Angle : 0.582 12.479 9215 Z= 0.284 Chirality : 0.044 0.252 987 Planarity : 0.004 0.057 1177 Dihedral : 10.486 76.932 1116 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.90 % Allowed : 22.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.31), residues: 790 helix: 1.62 (0.28), residues: 370 sheet: 0.49 (0.74), residues: 45 loop : -0.81 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 454 TYR 0.021 0.001 TYR A 521 PHE 0.008 0.001 PHE B 347 TRP 0.012 0.001 TRP A 203 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6744) covalent geometry : angle 0.56708 ( 9171) SS BOND : bond 0.00352 ( 7) SS BOND : angle 0.53984 ( 14) hydrogen bonds : bond 0.05183 ( 289) hydrogen bonds : angle 4.25009 ( 820) metal coordination : bond 0.39226 ( 2) link_BETA1-4 : bond 0.00413 ( 2) link_BETA1-4 : angle 0.83493 ( 6) link_BETA1-6 : bond 0.00290 ( 1) link_BETA1-6 : angle 1.37925 ( 3) link_NAG-ASN : bond 0.00685 ( 7) link_NAG-ASN : angle 2.74305 ( 21) *********************** 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 199 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.290 Fit side-chains REVERT: A 364 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8138 (t) outliers start: 34 outliers final: 25 residues processed: 182 average time/residue: 0.5201 time to fit residues: 99.9268 Evaluate side-chains 176 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 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 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 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 32 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.138518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.120130 restraints weight = 12225.764| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.35 r_work: 0.3554 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.0991 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= 0.150 Angle : 0.586 11.370 9215 Z= 0.284 Chirality : 0.045 0.316 987 Planarity : 0.004 0.059 1177 Dihedral : 7.438 59.625 1091 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.76 % Allowed : 22.05 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.30), residues: 790 helix: 1.58 (0.27), residues: 370 sheet: 0.28 (0.73), residues: 45 loop : -0.85 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 454 TYR 0.020 0.002 TYR A 521 PHE 0.011 0.001 PHE B 347 TRP 0.009 0.001 TRP A 203 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6744) covalent geometry : angle 0.56988 ( 9171) SS BOND : bond 0.00362 ( 7) SS BOND : angle 0.50745 ( 14) hydrogen bonds : bond 0.04970 ( 289) hydrogen bonds : angle 4.04286 ( 820) metal coordination : bond 0.01794 ( 2) link_BETA1-4 : bond 0.00344 ( 2) link_BETA1-4 : angle 0.86712 ( 6) link_BETA1-6 : bond 0.00289 ( 1) link_BETA1-6 : angle 1.34340 ( 3) link_NAG-ASN : bond 0.00655 ( 7) link_NAG-ASN : angle 2.82537 ( 21) *********************** 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 194 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.183 Fit side-chains REVERT: A 364 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8206 (t) REVERT: B 423 TYR cc_start: 0.8052 (t80) cc_final: 0.7832 (t80) outliers start: 40 outliers final: 27 residues processed: 171 average time/residue: 0.4986 time to fit residues: 89.5614 Evaluate side-chains 178 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 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 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 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 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 55 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.137987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.118211 restraints weight = 17746.077| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.90 r_work: 0.3509 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6763 Z= 0.153 Angle : 0.578 12.440 9215 Z= 0.283 Chirality : 0.045 0.321 987 Planarity : 0.004 0.060 1177 Dihedral : 6.512 54.701 1088 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.19 % Allowed : 23.20 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.30), residues: 790 helix: 1.58 (0.28), residues: 370 sheet: 0.39 (0.72), residues: 45 loop : -0.91 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 559 TYR 0.020 0.001 TYR A 521 PHE 0.009 0.001 PHE B 347 TRP 0.009 0.001 TRP A 203 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6744) covalent geometry : angle 0.56206 ( 9171) SS BOND : bond 0.00352 ( 7) SS BOND : angle 0.48376 ( 14) hydrogen bonds : bond 0.04885 ( 289) hydrogen bonds : angle 3.99848 ( 820) metal coordination : bond 0.00444 ( 2) link_BETA1-4 : bond 0.00361 ( 2) link_BETA1-4 : angle 0.86373 ( 6) link_BETA1-6 : bond 0.00240 ( 1) link_BETA1-6 : angle 1.42236 ( 3) link_NAG-ASN : bond 0.00642 ( 7) link_NAG-ASN : angle 2.85166 ( 21) *********************** 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 189 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.205 Fit side-chains REVERT: A 364 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8214 (t) REVERT: B 386 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7591 (tmmm) REVERT: B 424 LYS cc_start: 0.8021 (tppt) cc_final: 0.7728 (tppt) outliers start: 36 outliers final: 26 residues processed: 167 average time/residue: 0.5123 time to fit residues: 90.0853 Evaluate side-chains 175 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 132 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 GLU 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.137960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.119770 restraints weight = 11725.659| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.30 r_work: 0.3556 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6763 Z= 0.148 Angle : 0.575 11.828 9215 Z= 0.281 Chirality : 0.044 0.311 987 Planarity : 0.004 0.059 1177 Dihedral : 6.099 54.434 1085 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.33 % Allowed : 23.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.30), residues: 790 helix: 1.46 (0.27), residues: 376 sheet: 0.53 (0.73), residues: 45 loop : -1.00 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 192 TYR 0.020 0.001 TYR A 521 PHE 0.008 0.001 PHE A 72 TRP 0.009 0.001 TRP A 203 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6744) covalent geometry : angle 0.56031 ( 9171) SS BOND : bond 0.00346 ( 7) SS BOND : angle 0.48587 ( 14) hydrogen bonds : bond 0.04815 ( 289) hydrogen bonds : angle 3.95852 ( 820) metal coordination : bond 0.00208 ( 2) link_BETA1-4 : bond 0.00347 ( 2) link_BETA1-4 : angle 0.89371 ( 6) link_BETA1-6 : bond 0.00304 ( 1) link_BETA1-6 : angle 1.46778 ( 3) link_NAG-ASN : bond 0.00655 ( 7) link_NAG-ASN : angle 2.72394 ( 21) *********************** 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 195 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.181 Fit side-chains REVERT: A 197 GLU cc_start: 0.7341 (pm20) cc_final: 0.7099 (mp0) REVERT: A 364 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8223 (t) REVERT: B 386 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7199 (tmmm) REVERT: B 423 TYR cc_start: 0.8089 (t80) cc_final: 0.7885 (t80) outliers start: 37 outliers final: 26 residues processed: 174 average time/residue: 0.5592 time to fit residues: 102.3514 Evaluate side-chains 189 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 B 354 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.138234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.120191 restraints weight = 11236.049| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.24 r_work: 0.3560 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1300 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= 0.140 Angle : 0.579 12.426 9215 Z= 0.280 Chirality : 0.044 0.310 987 Planarity : 0.004 0.059 1177 Dihedral : 5.855 54.121 1083 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.33 % Allowed : 23.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.30), residues: 790 helix: 1.47 (0.27), residues: 376 sheet: 0.53 (0.73), residues: 45 loop : -1.01 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 192 TYR 0.021 0.001 TYR A 521 PHE 0.008 0.001 PHE A 72 TRP 0.010 0.001 TRP A 203 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6744) covalent geometry : angle 0.56381 ( 9171) SS BOND : bond 0.00322 ( 7) SS BOND : angle 0.46795 ( 14) hydrogen bonds : bond 0.04668 ( 289) hydrogen bonds : angle 3.93386 ( 820) metal coordination : bond 0.00207 ( 2) link_BETA1-4 : bond 0.00339 ( 2) link_BETA1-4 : angle 0.90148 ( 6) link_BETA1-6 : bond 0.00267 ( 1) link_BETA1-6 : angle 1.45765 ( 3) link_NAG-ASN : bond 0.00642 ( 7) link_NAG-ASN : angle 2.71904 ( 21) *********************** 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 200 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.253 Fit side-chains REVERT: A 197 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: A 364 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8216 (t) REVERT: B 386 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7180 (tmmm) outliers start: 37 outliers final: 28 residues processed: 178 average time/residue: 0.4930 time to fit residues: 92.7560 Evaluate side-chains 189 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 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 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 350 VAL 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 27 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 B 354 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 = 0.3899 r_free = 0.3899 target = 0.137754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.119102 restraints weight = 13101.329| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.45 r_work: 0.3538 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6763 Z= 0.154 Angle : 0.587 11.740 9215 Z= 0.287 Chirality : 0.045 0.314 987 Planarity : 0.004 0.059 1177 Dihedral : 5.827 54.456 1083 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.33 % Allowed : 23.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.30), residues: 790 helix: 1.45 (0.27), residues: 376 sheet: 0.60 (0.73), residues: 45 loop : -1.04 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 559 TYR 0.020 0.001 TYR A 521 PHE 0.008 0.001 PHE B 456 TRP 0.011 0.001 TRP A 203 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6744) covalent geometry : angle 0.57297 ( 9171) SS BOND : bond 0.00348 ( 7) SS BOND : angle 0.49459 ( 14) hydrogen bonds : bond 0.04865 ( 289) hydrogen bonds : angle 3.93543 ( 820) metal coordination : bond 0.00262 ( 2) link_BETA1-4 : bond 0.00378 ( 2) link_BETA1-4 : angle 0.95999 ( 6) link_BETA1-6 : bond 0.00239 ( 1) link_BETA1-6 : angle 1.49307 ( 3) link_NAG-ASN : bond 0.00639 ( 7) link_NAG-ASN : angle 2.70540 ( 21) *********************** 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 199 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.193 Fit side-chains REVERT: A 197 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: A 364 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8233 (t) REVERT: B 423 TYR cc_start: 0.8149 (t80) cc_final: 0.7942 (t80) REVERT: B 424 LYS cc_start: 0.8081 (tppt) cc_final: 0.7841 (tppt) outliers start: 37 outliers final: 28 residues processed: 175 average time/residue: 0.4890 time to fit residues: 90.1779 Evaluate side-chains 186 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 0.0670 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 B 448 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.138644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.121004 restraints weight = 11484.452| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.22 r_work: 0.3577 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1393 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= 0.124 Angle : 0.567 12.600 9215 Z= 0.274 Chirality : 0.043 0.300 987 Planarity : 0.004 0.057 1177 Dihedral : 5.542 53.242 1079 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.04 % Allowed : 24.50 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.30), residues: 790 helix: 1.53 (0.27), residues: 376 sheet: 0.55 (0.74), residues: 45 loop : -1.00 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 192 TYR 0.018 0.001 TYR A 521 PHE 0.009 0.001 PHE B 456 TRP 0.011 0.001 TRP A 203 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6744) covalent geometry : angle 0.55276 ( 9171) SS BOND : bond 0.00286 ( 7) SS BOND : angle 0.46739 ( 14) hydrogen bonds : bond 0.04386 ( 289) hydrogen bonds : angle 3.88264 ( 820) metal coordination : bond 0.00169 ( 2) link_BETA1-4 : bond 0.00390 ( 2) link_BETA1-4 : angle 0.92669 ( 6) link_BETA1-6 : bond 0.00242 ( 1) link_BETA1-6 : angle 1.43108 ( 3) link_NAG-ASN : bond 0.00598 ( 7) link_NAG-ASN : angle 2.59766 ( 21) *********************** 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 199 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.259 Fit side-chains REVERT: A 197 GLU cc_start: 0.7295 (pm20) cc_final: 0.7043 (mp0) REVERT: B 423 TYR cc_start: 0.8029 (t80) cc_final: 0.7823 (t80) REVERT: B 424 LYS cc_start: 0.8067 (tppt) cc_final: 0.7822 (tppt) outliers start: 35 outliers final: 28 residues processed: 177 average time/residue: 0.4646 time to fit residues: 86.9425 Evaluate side-chains 185 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.174 ------------------------------------------------------------------------------- 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 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 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 A residue 568 LEU Chi-restraints excluded: chain A residue 579 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.0370 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.7462 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.137945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.120088 restraints weight = 11508.363| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.24 r_work: 0.3566 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 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 = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6763 Z= 0.153 Angle : 0.608 12.674 9215 Z= 0.295 Chirality : 0.045 0.309 987 Planarity : 0.004 0.058 1177 Dihedral : 5.583 53.755 1077 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 5.04 % Allowed : 24.93 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.30), residues: 790 helix: 1.38 (0.27), residues: 382 sheet: 0.60 (0.73), residues: 45 loop : -1.08 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 559 TYR 0.022 0.001 TYR A 521 PHE 0.008 0.001 PHE A 72 TRP 0.011 0.001 TRP A 203 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6744) covalent geometry : angle 0.59151 ( 9171) SS BOND : bond 0.00363 ( 7) SS BOND : angle 1.72436 ( 14) hydrogen bonds : bond 0.04747 ( 289) hydrogen bonds : angle 3.91047 ( 820) metal coordination : bond 0.00191 ( 2) link_BETA1-4 : bond 0.00394 ( 2) link_BETA1-4 : angle 0.98537 ( 6) link_BETA1-6 : bond 0.00251 ( 1) link_BETA1-6 : angle 1.46672 ( 3) link_NAG-ASN : bond 0.00607 ( 7) link_NAG-ASN : angle 2.64507 ( 21) *********************** 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 197 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.246 Fit side-chains REVERT: A 197 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7055 (mp0) outliers start: 35 outliers final: 28 residues processed: 173 average time/residue: 0.4528 time to fit residues: 82.5349 Evaluate side-chains 189 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 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 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 A residue 579 MET 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 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 34 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 40 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.139126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.122088 restraints weight = 9265.406| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.98 r_work: 0.3600 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 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 = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6763 Z= 0.127 Angle : 0.587 12.856 9215 Z= 0.284 Chirality : 0.044 0.299 987 Planarity : 0.004 0.057 1177 Dihedral : 5.533 53.239 1077 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.18 % Allowed : 25.36 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.30), residues: 790 helix: 1.42 (0.27), residues: 382 sheet: 0.60 (0.74), residues: 45 loop : -1.07 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 559 TYR 0.021 0.001 TYR A 521 PHE 0.010 0.001 PHE B 456 TRP 0.012 0.001 TRP A 203 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6744) covalent geometry : angle 0.57156 ( 9171) SS BOND : bond 0.00272 ( 7) SS BOND : angle 1.46889 ( 14) hydrogen bonds : bond 0.04388 ( 289) hydrogen bonds : angle 3.88761 ( 820) metal coordination : bond 0.00209 ( 2) link_BETA1-4 : bond 0.00367 ( 2) link_BETA1-4 : angle 0.94922 ( 6) link_BETA1-6 : bond 0.00191 ( 1) link_BETA1-6 : angle 1.40118 ( 3) link_NAG-ASN : bond 0.00580 ( 7) link_NAG-ASN : angle 2.55702 ( 21) ********************** 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 192 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.268 Fit side-chains REVERT: A 197 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: B 424 LYS cc_start: 0.8047 (tppt) cc_final: 0.7830 (tppt) outliers start: 29 outliers final: 26 residues processed: 173 average time/residue: 0.5426 time to fit residues: 99.0827 Evaluate side-chains 188 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 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 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 A residue 579 MET 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 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 59 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 0.0570 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 B 448 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.139112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.120533 restraints weight = 13229.060| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.44 r_work: 0.3562 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6763 Z= 0.128 Angle : 0.587 12.806 9215 Z= 0.284 Chirality : 0.044 0.297 987 Planarity : 0.004 0.057 1177 Dihedral : 5.491 53.276 1077 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.18 % Allowed : 25.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.30), residues: 790 helix: 1.43 (0.27), residues: 382 sheet: 0.63 (0.74), residues: 45 loop : -1.07 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 559 TYR 0.021 0.001 TYR A 521 PHE 0.008 0.001 PHE B 456 TRP 0.013 0.001 TRP A 203 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6744) covalent geometry : angle 0.57297 ( 9171) SS BOND : bond 0.00273 ( 7) SS BOND : angle 1.21367 ( 14) hydrogen bonds : bond 0.04418 ( 289) hydrogen bonds : angle 3.87447 ( 820) metal coordination : bond 0.00177 ( 2) link_BETA1-4 : bond 0.00400 ( 2) link_BETA1-4 : angle 0.95982 ( 6) link_BETA1-6 : bond 0.00264 ( 1) link_BETA1-6 : angle 1.42958 ( 3) link_NAG-ASN : bond 0.00583 ( 7) link_NAG-ASN : angle 2.50263 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3413.51 seconds wall clock time: 58 minutes 34.14 seconds (3514.14 seconds total)