Starting phenix.real_space_refine on Tue May 13 15:41:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xv0_38688/05_2025/8xv0_38688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xv0_38688/05_2025/8xv0_38688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xv0_38688/05_2025/8xv0_38688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xv0_38688/05_2025/8xv0_38688.map" model { file = "/net/cci-nas-00/data/ceres_data/8xv0_38688/05_2025/8xv0_38688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xv0_38688/05_2025/8xv0_38688.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.034 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 4904 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4241 2.51 5 N 1078 2.21 5 O 1277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6633 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} 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: 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: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" 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: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.63, per 1000 atoms: 0.70 Number of scatterers: 6633 At special positions: 0 Unit cell: (87.435, 86.43, 118.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1277 8.00 N 1078 7.00 C 4241 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 524 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 487 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 701 " - " ASN A 322 " " NAG A 702 " - " ASN A 432 " " NAG B1300 " - " ASN B 343 " " NAG B1301 " - " ASN B 354 " " NAG C 1 " - " ASN A 53 " " NAG D 1 " - " ASN A 546 " " NAG E 1 " - " ASN A 90 " " NAG F 1 " - " ASN A 103 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 812.1 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 55.9% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.520A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 38 " --> pdb=" O HIS 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: 3.968A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 174 Processing helix chain 'A' and resid 176 through 194 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 4.117A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.876A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.501A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.782A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.569A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 4.045A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.711A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.345A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.719A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.511A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.515A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.092A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.651A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.105A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.686A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN B 394 " --> pdb=" O GLU B 515 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU B 515 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 307 hydrogen bonds defined for protein. 879 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: 1.76 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2083 1.34 - 1.46: 1770 1.46 - 1.58: 2910 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6821 Sorted by residual: bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.554 -0.028 2.00e-02 2.50e+03 1.90e+00 ... (remaining 6816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 8956 1.28 - 2.56: 225 2.56 - 3.84: 57 3.84 - 5.12: 26 5.12 - 6.39: 7 Bond angle restraints: 9271 Sorted by residual: angle pdb=" C PRO A 135 " pdb=" N ASP A 136 " pdb=" CA ASP A 136 " ideal model delta sigma weight residual 121.54 125.96 -4.42 1.91e+00 2.74e-01 5.36e+00 angle pdb=" CA ASP A 136 " pdb=" CB ASP A 136 " pdb=" CG ASP A 136 " ideal model delta sigma weight residual 112.60 114.88 -2.28 1.00e+00 1.00e+00 5.20e+00 angle pdb=" CA CYS B 391 " pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 114.40 119.39 -4.99 2.30e+00 1.89e-01 4.70e+00 angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.56 6.39 3.00e+00 1.11e-01 4.54e+00 angle pdb=" C3 MAN F 5 " pdb=" C2 MAN F 5 " pdb=" O2 MAN F 5 " ideal model delta sigma weight residual 111.77 105.39 6.38 3.00e+00 1.11e-01 4.52e+00 ... (remaining 9266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.00: 3964 22.00 - 44.00: 220 44.00 - 66.00: 15 66.00 - 88.01: 16 88.01 - 110.01: 9 Dihedral angle restraints: 4224 sinusoidal: 1903 harmonic: 2321 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 524 " pdb=" CB CYS B 524 " ideal model delta sinusoidal sigma weight residual 93.00 8.76 84.24 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -129.66 43.66 1 1.00e+01 1.00e-02 2.66e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.70 110.01 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 4221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 1008 0.142 - 0.284: 4 0.284 - 0.426: 1 0.426 - 0.569: 0 0.569 - 0.711: 1 Chirality restraints: 1014 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1011 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 103 " -0.018 2.00e-02 2.50e+03 1.73e-02 3.75e+00 pdb=" CG ASN A 103 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 103 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 103 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 226 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C VAL A 226 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL A 226 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A 227 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 241 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C HIS A 241 " 0.028 2.00e-02 2.50e+03 pdb=" O HIS A 241 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA A 242 " -0.009 2.00e-02 2.50e+03 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1320 2.77 - 3.31: 6166 3.31 - 3.84: 10591 3.84 - 4.37: 11686 4.37 - 4.90: 20940 Nonbonded interactions: 50703 Sorted by model distance: nonbonded pdb=" OG SER A 563 " pdb=" OE1 GLU A 564 " model vdw 2.242 3.040 nonbonded pdb=" OG SER A 611 " pdb=" O ALA A 614 " model vdw 2.242 3.040 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.276 3.120 nonbonded pdb=" O MET A 152 " pdb=" NH1 ARG A 161 " model vdw 2.305 3.120 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.318 3.120 ... (remaining 50698 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.630 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 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 : 0.003 0.031 6844 Z= 0.160 Angle : 0.600 8.265 9333 Z= 0.283 Chirality : 0.049 0.711 1014 Planarity : 0.003 0.025 1175 Dihedral : 14.697 110.007 2713 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.31), residues: 786 helix: 1.87 (0.28), residues: 395 sheet: 1.62 (0.81), residues: 44 loop : -0.71 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 203 HIS 0.003 0.001 HIS A 401 PHE 0.010 0.001 PHE B 347 TYR 0.023 0.001 TYR A 199 ARG 0.003 0.000 ARG A 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00712 ( 8) link_NAG-ASN : angle 3.60831 ( 24) link_ALPHA1-6 : bond 0.00409 ( 1) link_ALPHA1-6 : angle 1.60825 ( 3) link_BETA1-4 : bond 0.00327 ( 6) link_BETA1-4 : angle 1.95543 ( 18) link_ALPHA1-3 : bond 0.00401 ( 1) link_ALPHA1-3 : angle 1.47651 ( 3) hydrogen bonds : bond 0.15650 ( 307) hydrogen bonds : angle 6.12422 ( 879) SS BOND : bond 0.00119 ( 7) SS BOND : angle 1.76926 ( 14) covalent geometry : bond 0.00320 ( 6821) covalent geometry : angle 0.56093 ( 9271) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.801 Fit side-chains REVERT: A 37 GLU cc_start: 0.6388 (mt-10) cc_final: 0.5950 (mt-10) REVERT: A 81 GLN cc_start: 0.7959 (mt0) cc_final: 0.7191 (mm110) REVERT: A 182 GLU cc_start: 0.6543 (tt0) cc_final: 0.6203 (mp0) REVERT: A 190 MET cc_start: 0.5700 (tmm) cc_final: 0.5209 (tmm) REVERT: A 231 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6280 (mt-10) REVERT: A 295 ASP cc_start: 0.5526 (m-30) cc_final: 0.5216 (m-30) REVERT: A 441 LYS cc_start: 0.6526 (tttt) cc_final: 0.6256 (ttpp) REVERT: A 546 ASN cc_start: 0.6704 (m110) cc_final: 0.5429 (p0) REVERT: A 579 MET cc_start: 0.7122 (mtm) cc_final: 0.6827 (mtm) REVERT: A 585 LEU cc_start: 0.6637 (mt) cc_final: 0.6425 (mm) REVERT: B 357 ARG cc_start: 0.7716 (ttp80) cc_final: 0.6958 (ttt-90) REVERT: B 378 LYS cc_start: 0.6314 (mmtt) cc_final: 0.5556 (tptp) REVERT: B 394 ASN cc_start: 0.6702 (m110) cc_final: 0.6289 (m110) REVERT: B 440 LYS cc_start: 0.7498 (tmtt) cc_final: 0.7255 (mptt) REVERT: B 462 LYS cc_start: 0.7046 (mmtp) cc_final: 0.6711 (mppt) REVERT: B 468 ILE cc_start: 0.8069 (mt) cc_final: 0.7848 (mm) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 1.2076 time to fit residues: 190.3416 Evaluate side-chains 90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 0.0370 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 121 ASN A 210 ASN A 531 GLN B 388 ASN B 486 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.166531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.134696 restraints weight = 7848.000| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.04 r_work: 0.3359 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6844 Z= 0.137 Angle : 0.619 10.726 9333 Z= 0.301 Chirality : 0.044 0.319 1014 Planarity : 0.004 0.032 1175 Dihedral : 10.687 78.288 1185 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.45 % Allowed : 10.37 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.31), residues: 786 helix: 2.00 (0.27), residues: 405 sheet: 1.53 (0.81), residues: 42 loop : -0.68 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS A 535 PHE 0.016 0.001 PHE B 347 TYR 0.015 0.001 TYR A 199 ARG 0.005 0.001 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.01139 ( 8) link_NAG-ASN : angle 4.35136 ( 24) link_ALPHA1-6 : bond 0.00339 ( 1) link_ALPHA1-6 : angle 1.76335 ( 3) link_BETA1-4 : bond 0.00364 ( 6) link_BETA1-4 : angle 2.12925 ( 18) link_ALPHA1-3 : bond 0.01324 ( 1) link_ALPHA1-3 : angle 2.08040 ( 3) hydrogen bonds : bond 0.05443 ( 307) hydrogen bonds : angle 4.34878 ( 879) SS BOND : bond 0.00171 ( 7) SS BOND : angle 1.70486 ( 14) covalent geometry : bond 0.00286 ( 6821) covalent geometry : angle 0.56712 ( 9271) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7347 (mt-10) REVERT: A 81 GLN cc_start: 0.8151 (mt0) cc_final: 0.7813 (mm110) REVERT: A 131 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7204 (ttmt) REVERT: A 190 MET cc_start: 0.7140 (tmm) cc_final: 0.6523 (tmm) REVERT: A 295 ASP cc_start: 0.7133 (m-30) cc_final: 0.6787 (m-30) REVERT: A 376 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8193 (mmt) REVERT: A 527 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7277 (tt0) REVERT: A 546 ASN cc_start: 0.7415 (m110) cc_final: 0.6406 (p0) REVERT: A 579 MET cc_start: 0.7846 (mtm) cc_final: 0.7429 (mtm) REVERT: B 378 LYS cc_start: 0.7505 (mmtt) cc_final: 0.7227 (tptp) outliers start: 17 outliers final: 8 residues processed: 106 average time/residue: 1.1762 time to fit residues: 131.2110 Evaluate side-chains 94 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN B 388 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.164147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.133435 restraints weight = 7938.118| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.12 r_work: 0.3217 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6844 Z= 0.182 Angle : 0.645 9.919 9333 Z= 0.320 Chirality : 0.047 0.341 1014 Planarity : 0.004 0.036 1175 Dihedral : 9.721 76.053 1185 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.31 % Allowed : 13.26 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.31), residues: 786 helix: 1.91 (0.27), residues: 400 sheet: 0.70 (0.71), residues: 52 loop : -0.74 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.004 0.001 HIS A 540 PHE 0.021 0.002 PHE B 347 TYR 0.019 0.002 TYR A 385 ARG 0.006 0.001 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 8) link_NAG-ASN : angle 3.56643 ( 24) link_ALPHA1-6 : bond 0.00392 ( 1) link_ALPHA1-6 : angle 1.66374 ( 3) link_BETA1-4 : bond 0.00396 ( 6) link_BETA1-4 : angle 2.43788 ( 18) link_ALPHA1-3 : bond 0.01390 ( 1) link_ALPHA1-3 : angle 1.69816 ( 3) hydrogen bonds : bond 0.06465 ( 307) hydrogen bonds : angle 4.29775 ( 879) SS BOND : bond 0.00224 ( 7) SS BOND : angle 2.00833 ( 14) covalent geometry : bond 0.00420 ( 6821) covalent geometry : angle 0.60585 ( 9271) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7626 (mt-10) REVERT: A 81 GLN cc_start: 0.8395 (mt0) cc_final: 0.7969 (mm110) REVERT: A 131 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7338 (ttmt) REVERT: A 190 MET cc_start: 0.7224 (tmm) cc_final: 0.6378 (tmm) REVERT: A 295 ASP cc_start: 0.7203 (m-30) cc_final: 0.6840 (m-30) REVERT: A 401 HIS cc_start: 0.8037 (OUTLIER) cc_final: 0.7752 (m-70) REVERT: A 527 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: A 579 MET cc_start: 0.7845 (mtm) cc_final: 0.7465 (mtm) REVERT: B 378 LYS cc_start: 0.7543 (mmtt) cc_final: 0.7331 (tptp) REVERT: B 462 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7534 (mtpt) outliers start: 16 outliers final: 8 residues processed: 94 average time/residue: 1.1484 time to fit residues: 114.3604 Evaluate side-chains 89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 462 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 69 optimal weight: 0.0670 chunk 12 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 121 ASN A 287 GLN B 388 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.161545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.129154 restraints weight = 7921.793| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.22 r_work: 0.3263 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6844 Z= 0.164 Angle : 0.635 10.183 9333 Z= 0.313 Chirality : 0.047 0.355 1014 Planarity : 0.004 0.034 1175 Dihedral : 8.748 75.231 1185 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.03 % Allowed : 13.83 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.30), residues: 786 helix: 1.83 (0.27), residues: 399 sheet: 0.70 (0.70), residues: 52 loop : -0.81 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.005 0.001 HIS A 540 PHE 0.016 0.002 PHE B 347 TYR 0.018 0.002 TYR A 385 ARG 0.004 0.001 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 8) link_NAG-ASN : angle 3.70276 ( 24) link_ALPHA1-6 : bond 0.00379 ( 1) link_ALPHA1-6 : angle 1.53592 ( 3) link_BETA1-4 : bond 0.00495 ( 6) link_BETA1-4 : angle 2.56790 ( 18) link_ALPHA1-3 : bond 0.01408 ( 1) link_ALPHA1-3 : angle 1.76919 ( 3) hydrogen bonds : bond 0.06205 ( 307) hydrogen bonds : angle 4.26504 ( 879) SS BOND : bond 0.00192 ( 7) SS BOND : angle 1.90674 ( 14) covalent geometry : bond 0.00371 ( 6821) covalent geometry : angle 0.59233 ( 9271) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7617 (mt-10) REVERT: A 81 GLN cc_start: 0.8389 (mt0) cc_final: 0.8049 (mm110) REVERT: A 131 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7274 (ttmt) REVERT: A 156 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7360 (tt) REVERT: A 190 MET cc_start: 0.7179 (tmm) cc_final: 0.6318 (tmm) REVERT: A 224 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7088 (mm-30) REVERT: A 295 ASP cc_start: 0.6969 (m-30) cc_final: 0.6615 (m-30) REVERT: A 401 HIS cc_start: 0.8222 (OUTLIER) cc_final: 0.7639 (m-70) REVERT: A 527 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: A 546 ASN cc_start: 0.7271 (m110) cc_final: 0.6212 (p0) REVERT: A 579 MET cc_start: 0.7895 (mtm) cc_final: 0.7560 (mtm) REVERT: A 600 LYS cc_start: 0.7743 (pttm) cc_final: 0.7416 (pttt) REVERT: B 378 LYS cc_start: 0.7491 (mmtt) cc_final: 0.7217 (tptp) REVERT: B 417 ASN cc_start: 0.7966 (t160) cc_final: 0.7733 (t0) REVERT: B 440 LYS cc_start: 0.8636 (ttpp) cc_final: 0.8168 (mptt) REVERT: B 462 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7533 (mtpt) outliers start: 28 outliers final: 14 residues processed: 97 average time/residue: 1.0671 time to fit residues: 109.8015 Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 462 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 287 GLN B 388 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.162816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.130622 restraints weight = 7831.449| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.15 r_work: 0.3258 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6844 Z= 0.127 Angle : 0.573 9.122 9333 Z= 0.282 Chirality : 0.044 0.323 1014 Planarity : 0.003 0.030 1175 Dihedral : 7.780 71.915 1185 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.60 % Allowed : 14.27 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.31), residues: 786 helix: 2.00 (0.27), residues: 398 sheet: 0.85 (0.70), residues: 52 loop : -0.81 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 540 PHE 0.010 0.001 PHE B 347 TYR 0.013 0.001 TYR A 385 ARG 0.004 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00782 ( 8) link_NAG-ASN : angle 3.42869 ( 24) link_ALPHA1-6 : bond 0.00543 ( 1) link_ALPHA1-6 : angle 1.52262 ( 3) link_BETA1-4 : bond 0.00441 ( 6) link_BETA1-4 : angle 2.20985 ( 18) link_ALPHA1-3 : bond 0.01242 ( 1) link_ALPHA1-3 : angle 1.78314 ( 3) hydrogen bonds : bond 0.05400 ( 307) hydrogen bonds : angle 4.20113 ( 879) SS BOND : bond 0.00128 ( 7) SS BOND : angle 1.66681 ( 14) covalent geometry : bond 0.00269 ( 6821) covalent geometry : angle 0.53387 ( 9271) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7430 (mt-10) REVERT: A 81 GLN cc_start: 0.8511 (mt0) cc_final: 0.8151 (mm110) REVERT: A 131 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7226 (ttmt) REVERT: A 190 MET cc_start: 0.7153 (tmm) cc_final: 0.6296 (tmm) REVERT: A 295 ASP cc_start: 0.6980 (m-30) cc_final: 0.6620 (m-30) REVERT: A 376 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8087 (mmt) REVERT: A 401 HIS cc_start: 0.8123 (OUTLIER) cc_final: 0.7576 (m-70) REVERT: A 527 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: A 546 ASN cc_start: 0.7220 (m110) cc_final: 0.6289 (p0) REVERT: A 571 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: A 579 MET cc_start: 0.7815 (mtm) cc_final: 0.7536 (mtm) REVERT: B 378 LYS cc_start: 0.7451 (mmtt) cc_final: 0.7249 (tmtt) REVERT: B 417 ASN cc_start: 0.7923 (t160) cc_final: 0.7671 (t0) REVERT: B 462 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7450 (mtpt) outliers start: 25 outliers final: 9 residues processed: 100 average time/residue: 1.0461 time to fit residues: 110.9611 Evaluate side-chains 94 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 462 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN B 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.162143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130142 restraints weight = 7836.068| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.16 r_work: 0.3259 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6844 Z= 0.136 Angle : 0.588 9.255 9333 Z= 0.289 Chirality : 0.044 0.332 1014 Planarity : 0.003 0.029 1175 Dihedral : 7.522 70.275 1185 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.46 % Allowed : 15.42 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.31), residues: 786 helix: 1.98 (0.27), residues: 398 sheet: 0.92 (0.71), residues: 52 loop : -0.83 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.003 0.001 HIS A 540 PHE 0.009 0.001 PHE B 371 TYR 0.014 0.001 TYR A 385 ARG 0.003 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 8) link_NAG-ASN : angle 3.39243 ( 24) link_ALPHA1-6 : bond 0.00601 ( 1) link_ALPHA1-6 : angle 1.49310 ( 3) link_BETA1-4 : bond 0.00433 ( 6) link_BETA1-4 : angle 2.14026 ( 18) link_ALPHA1-3 : bond 0.01239 ( 1) link_ALPHA1-3 : angle 1.74108 ( 3) hydrogen bonds : bond 0.05603 ( 307) hydrogen bonds : angle 4.21443 ( 879) SS BOND : bond 0.00131 ( 7) SS BOND : angle 1.85351 ( 14) covalent geometry : bond 0.00297 ( 6821) covalent geometry : angle 0.55017 ( 9271) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7372 (mt-10) REVERT: A 81 GLN cc_start: 0.8528 (mt0) cc_final: 0.8166 (mm110) REVERT: A 131 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7202 (ttmt) REVERT: A 190 MET cc_start: 0.7141 (tmm) cc_final: 0.6287 (tmm) REVERT: A 224 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.7027 (mm-30) REVERT: A 295 ASP cc_start: 0.6963 (m-30) cc_final: 0.6591 (m-30) REVERT: A 527 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: A 546 ASN cc_start: 0.7247 (m110) cc_final: 0.6291 (p0) REVERT: A 579 MET cc_start: 0.7843 (mtm) cc_final: 0.7535 (mtm) REVERT: B 378 LYS cc_start: 0.7452 (mmtt) cc_final: 0.7227 (tmtt) REVERT: B 417 ASN cc_start: 0.7934 (t160) cc_final: 0.7695 (t0) REVERT: B 440 LYS cc_start: 0.8638 (ttpp) cc_final: 0.8135 (mptt) REVERT: B 462 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7460 (mtpt) outliers start: 24 outliers final: 10 residues processed: 98 average time/residue: 1.0457 time to fit residues: 108.6819 Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 462 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 20 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN B 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.161783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129665 restraints weight = 7875.129| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.20 r_work: 0.3269 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6844 Z= 0.140 Angle : 0.592 9.263 9333 Z= 0.293 Chirality : 0.044 0.334 1014 Planarity : 0.004 0.031 1175 Dihedral : 7.340 68.211 1185 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.88 % Allowed : 15.71 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.31), residues: 786 helix: 2.02 (0.27), residues: 393 sheet: 0.87 (0.71), residues: 52 loop : -0.87 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.004 0.001 HIS A 540 PHE 0.014 0.001 PHE B 371 TYR 0.015 0.001 TYR A 385 ARG 0.002 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00621 ( 8) link_NAG-ASN : angle 3.33698 ( 24) link_ALPHA1-6 : bond 0.00717 ( 1) link_ALPHA1-6 : angle 1.48176 ( 3) link_BETA1-4 : bond 0.00435 ( 6) link_BETA1-4 : angle 2.06976 ( 18) link_ALPHA1-3 : bond 0.01323 ( 1) link_ALPHA1-3 : angle 1.81652 ( 3) hydrogen bonds : bond 0.05687 ( 307) hydrogen bonds : angle 4.20728 ( 879) SS BOND : bond 0.00136 ( 7) SS BOND : angle 1.79716 ( 14) covalent geometry : bond 0.00309 ( 6821) covalent geometry : angle 0.55613 ( 9271) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7505 (mt-10) REVERT: A 81 GLN cc_start: 0.8531 (mt0) cc_final: 0.8176 (mm110) REVERT: A 131 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7203 (ttmt) REVERT: A 156 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7307 (tt) REVERT: A 190 MET cc_start: 0.7162 (tmm) cc_final: 0.6300 (tmm) REVERT: A 295 ASP cc_start: 0.7070 (m-30) cc_final: 0.6689 (m-30) REVERT: A 401 HIS cc_start: 0.8269 (OUTLIER) cc_final: 0.7533 (m-70) REVERT: A 527 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: A 546 ASN cc_start: 0.7233 (m110) cc_final: 0.6291 (p0) REVERT: A 579 MET cc_start: 0.7841 (mtm) cc_final: 0.7529 (mtm) REVERT: B 417 ASN cc_start: 0.7930 (t160) cc_final: 0.7703 (t0) REVERT: B 462 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7478 (mtpt) outliers start: 20 outliers final: 11 residues processed: 96 average time/residue: 1.0672 time to fit residues: 108.5480 Evaluate side-chains 96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 462 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.161864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130093 restraints weight = 7895.344| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.17 r_work: 0.3192 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6844 Z= 0.141 Angle : 0.598 8.939 9333 Z= 0.295 Chirality : 0.044 0.321 1014 Planarity : 0.004 0.028 1175 Dihedral : 7.255 66.906 1185 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.17 % Allowed : 15.99 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.31), residues: 786 helix: 1.90 (0.27), residues: 395 sheet: 0.82 (0.70), residues: 52 loop : -0.91 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.003 0.001 HIS A 540 PHE 0.012 0.001 PHE B 371 TYR 0.014 0.001 TYR A 385 ARG 0.002 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 8) link_NAG-ASN : angle 3.30546 ( 24) link_ALPHA1-6 : bond 0.00682 ( 1) link_ALPHA1-6 : angle 1.41961 ( 3) link_BETA1-4 : bond 0.00443 ( 6) link_BETA1-4 : angle 2.05661 ( 18) link_ALPHA1-3 : bond 0.01283 ( 1) link_ALPHA1-3 : angle 1.80845 ( 3) hydrogen bonds : bond 0.05748 ( 307) hydrogen bonds : angle 4.24643 ( 879) SS BOND : bond 0.00122 ( 7) SS BOND : angle 1.78843 ( 14) covalent geometry : bond 0.00314 ( 6821) covalent geometry : angle 0.56267 ( 9271) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7493 (mt-10) REVERT: A 81 GLN cc_start: 0.8570 (mt0) cc_final: 0.8198 (mm110) REVERT: A 82 MET cc_start: 0.8312 (mtm) cc_final: 0.8103 (mtp) REVERT: A 131 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7097 (ttmt) REVERT: A 156 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7278 (tt) REVERT: A 190 MET cc_start: 0.7065 (tmm) cc_final: 0.6172 (tmm) REVERT: A 295 ASP cc_start: 0.7063 (m-30) cc_final: 0.6676 (m-30) REVERT: A 401 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7618 (m-70) REVERT: A 527 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7375 (tt0) REVERT: A 571 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: A 579 MET cc_start: 0.7812 (mtm) cc_final: 0.7503 (mtm) REVERT: B 417 ASN cc_start: 0.7927 (t160) cc_final: 0.7703 (t0) REVERT: B 440 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8101 (mmtm) REVERT: B 462 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7473 (mtpt) outliers start: 22 outliers final: 12 residues processed: 96 average time/residue: 1.1693 time to fit residues: 118.3590 Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 462 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.0070 chunk 11 optimal weight: 9.9990 chunk 72 optimal weight: 0.0050 chunk 47 optimal weight: 20.0000 chunk 55 optimal weight: 0.0980 overall best weight: 0.3412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.164774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.133274 restraints weight = 7874.818| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.05 r_work: 0.3307 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6844 Z= 0.113 Angle : 0.569 8.195 9333 Z= 0.278 Chirality : 0.043 0.310 1014 Planarity : 0.003 0.028 1175 Dihedral : 6.839 62.421 1185 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.03 % Allowed : 16.57 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.31), residues: 786 helix: 2.01 (0.27), residues: 401 sheet: 0.94 (0.70), residues: 52 loop : -0.77 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.002 0.001 HIS A 540 PHE 0.009 0.001 PHE A 327 TYR 0.008 0.001 TYR A 385 ARG 0.002 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.01143 ( 8) link_NAG-ASN : angle 3.17357 ( 24) link_ALPHA1-6 : bond 0.00789 ( 1) link_ALPHA1-6 : angle 1.49895 ( 3) link_BETA1-4 : bond 0.00578 ( 6) link_BETA1-4 : angle 2.03592 ( 18) link_ALPHA1-3 : bond 0.01175 ( 1) link_ALPHA1-3 : angle 1.80834 ( 3) hydrogen bonds : bond 0.04756 ( 307) hydrogen bonds : angle 4.18548 ( 879) SS BOND : bond 0.00076 ( 7) SS BOND : angle 1.56369 ( 14) covalent geometry : bond 0.00221 ( 6821) covalent geometry : angle 0.53555 ( 9271) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7305 (mt-10) REVERT: A 81 GLN cc_start: 0.8495 (mt0) cc_final: 0.8184 (mm110) REVERT: A 131 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7119 (ttmt) REVERT: A 156 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7256 (tt) REVERT: A 190 MET cc_start: 0.7207 (tmm) cc_final: 0.6386 (tmm) REVERT: A 224 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.7001 (mm-30) REVERT: A 295 ASP cc_start: 0.7186 (m-30) cc_final: 0.6797 (m-30) REVERT: A 401 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.7799 (m-70) REVERT: A 546 ASN cc_start: 0.6532 (m110) cc_final: 0.5826 (p0) REVERT: A 571 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: A 579 MET cc_start: 0.7642 (mtm) cc_final: 0.7355 (mtm) REVERT: B 440 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8120 (mmtm) REVERT: B 462 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7389 (mtpt) outliers start: 21 outliers final: 11 residues processed: 94 average time/residue: 1.0928 time to fit residues: 108.5972 Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 462 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.0000 chunk 22 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.163821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131736 restraints weight = 7962.188| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.18 r_work: 0.3273 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6844 Z= 0.121 Angle : 0.574 8.219 9333 Z= 0.282 Chirality : 0.043 0.314 1014 Planarity : 0.003 0.029 1175 Dihedral : 6.689 59.954 1185 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.02 % Allowed : 17.87 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.30), residues: 786 helix: 1.92 (0.27), residues: 403 sheet: 0.97 (0.70), residues: 52 loop : -0.80 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 540 PHE 0.009 0.001 PHE B 371 TYR 0.011 0.001 TYR A 385 ARG 0.002 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00774 ( 8) link_NAG-ASN : angle 3.06682 ( 24) link_ALPHA1-6 : bond 0.00805 ( 1) link_ALPHA1-6 : angle 1.43273 ( 3) link_BETA1-4 : bond 0.00518 ( 6) link_BETA1-4 : angle 1.86853 ( 18) link_ALPHA1-3 : bond 0.01243 ( 1) link_ALPHA1-3 : angle 1.85217 ( 3) hydrogen bonds : bond 0.05086 ( 307) hydrogen bonds : angle 4.17974 ( 879) SS BOND : bond 0.00096 ( 7) SS BOND : angle 1.61960 ( 14) covalent geometry : bond 0.00257 ( 6821) covalent geometry : angle 0.54259 ( 9271) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7377 (mt-10) REVERT: A 81 GLN cc_start: 0.8525 (mt0) cc_final: 0.8184 (mm110) REVERT: A 131 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7020 (ttmt) REVERT: A 156 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7223 (tt) REVERT: A 190 MET cc_start: 0.7153 (tmm) cc_final: 0.6264 (tmm) REVERT: A 295 ASP cc_start: 0.7172 (m-30) cc_final: 0.6782 (m-30) REVERT: A 401 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7765 (m-70) REVERT: A 546 ASN cc_start: 0.6146 (m110) cc_final: 0.5638 (p0) REVERT: A 571 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: A 579 MET cc_start: 0.7671 (mtm) cc_final: 0.7378 (mtm) REVERT: B 417 ASN cc_start: 0.7891 (t160) cc_final: 0.7660 (t0) REVERT: B 440 LYS cc_start: 0.8622 (ttpp) cc_final: 0.8152 (mmtm) REVERT: B 462 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7414 (mtpt) outliers start: 14 outliers final: 9 residues processed: 93 average time/residue: 1.0632 time to fit residues: 104.7448 Evaluate side-chains 95 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 518 ARG Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 462 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 10 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.163059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.131391 restraints weight = 7883.272| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.13 r_work: 0.3234 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6844 Z= 0.129 Angle : 0.580 8.088 9333 Z= 0.286 Chirality : 0.044 0.304 1014 Planarity : 0.003 0.030 1175 Dihedral : 6.571 56.149 1185 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.31 % Allowed : 18.16 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.30), residues: 786 helix: 1.98 (0.27), residues: 398 sheet: 0.97 (0.70), residues: 52 loop : -0.88 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.003 0.001 HIS A 540 PHE 0.011 0.001 PHE B 371 TYR 0.013 0.001 TYR A 385 ARG 0.003 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00697 ( 8) link_NAG-ASN : angle 3.08496 ( 24) link_ALPHA1-6 : bond 0.00799 ( 1) link_ALPHA1-6 : angle 1.31864 ( 3) link_BETA1-4 : bond 0.00519 ( 6) link_BETA1-4 : angle 1.89041 ( 18) link_ALPHA1-3 : bond 0.01295 ( 1) link_ALPHA1-3 : angle 1.89648 ( 3) hydrogen bonds : bond 0.05326 ( 307) hydrogen bonds : angle 4.19347 ( 879) SS BOND : bond 0.00107 ( 7) SS BOND : angle 1.67203 ( 14) covalent geometry : bond 0.00280 ( 6821) covalent geometry : angle 0.54927 ( 9271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5205.61 seconds wall clock time: 90 minutes 9.47 seconds (5409.47 seconds total)