Starting phenix.real_space_refine on Sat Nov 16 08:25:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv0_38688/11_2024/8xv0_38688.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv0_38688/11_2024/8xv0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv0_38688/11_2024/8xv0_38688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv0_38688/11_2024/8xv0_38688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv0_38688/11_2024/8xv0_38688.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv0_38688/11_2024/8xv0_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-5513/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: 5.11, per 1000 atoms: 0.77 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: 1.98 Conformation dependent library (CDL) restraints added in 930.3 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: 0.70 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: 1.78 Time building geometry restraints manager: 2.05 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: 3.640 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.850 Find NCS groups from input model: 0.060 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:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.970 ------------------------------------------------------------------------------- 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 6821 Z= 0.212 Angle : 0.561 6.395 9271 Z= 0.274 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 *********************** 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 : 0.815 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: 1.2848 time to fit residues: 201.8318 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 : 0.530 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 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 6821 Z= 0.190 Angle : 0.567 8.792 9271 Z= 0.289 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 *********************** 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 : 0.776 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6296 (mt-10) cc_final: 0.5881 (mt-10) REVERT: A 81 GLN cc_start: 0.8038 (mt0) cc_final: 0.7163 (mm110) REVERT: A 131 LYS cc_start: 0.6652 (OUTLIER) cc_final: 0.6308 (ttmt) REVERT: A 190 MET cc_start: 0.5455 (tmm) cc_final: 0.4942 (tmm) REVERT: A 231 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6579 (mt-10) REVERT: A 295 ASP cc_start: 0.5507 (m-30) cc_final: 0.5212 (m-30) REVERT: A 441 LYS cc_start: 0.6468 (tttt) cc_final: 0.6194 (ttpp) REVERT: A 527 GLU cc_start: 0.5660 (OUTLIER) cc_final: 0.5183 (tt0) REVERT: A 546 ASN cc_start: 0.6843 (m110) cc_final: 0.5580 (p0) REVERT: A 579 MET cc_start: 0.7244 (mtm) cc_final: 0.6811 (mtm) REVERT: A 585 LEU cc_start: 0.6641 (mt) cc_final: 0.6418 (mm) REVERT: B 357 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7222 (ttt180) REVERT: B 378 LYS cc_start: 0.6366 (mmtt) cc_final: 0.5684 (tptp) REVERT: B 440 LYS cc_start: 0.7554 (tmtt) cc_final: 0.7241 (mptt) REVERT: B 462 LYS cc_start: 0.6999 (mmtp) cc_final: 0.6700 (mppt) REVERT: B 468 ILE cc_start: 0.8206 (mt) cc_final: 0.7852 (mm) outliers start: 17 outliers final: 8 residues processed: 106 average time/residue: 1.3061 time to fit residues: 145.4107 Evaluate side-chains 95 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6821 Z= 0.203 Angle : 0.560 7.267 9271 Z= 0.288 Chirality : 0.045 0.343 1014 Planarity : 0.004 0.041 1175 Dihedral : 8.914 72.978 1185 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.31 % Allowed : 12.54 % Favored : 85.16 % 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: 1.24 (0.31), residues: 786 helix: 2.03 (0.27), residues: 400 sheet: 0.81 (0.71), residues: 52 loop : -0.70 (0.34), 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 0.022 0.002 PHE B 347 TYR 0.017 0.002 TYR A 385 ARG 0.002 0.000 ARG B 497 *********************** 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 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6446 (mt-10) cc_final: 0.6026 (mt-10) REVERT: A 81 GLN cc_start: 0.8198 (mt0) cc_final: 0.7300 (mm110) REVERT: A 131 LYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6389 (ttmt) REVERT: A 190 MET cc_start: 0.5413 (tmm) cc_final: 0.4685 (tmm) REVERT: A 231 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6695 (mt-10) REVERT: A 295 ASP cc_start: 0.5566 (m-30) cc_final: 0.5260 (m-30) REVERT: A 441 LYS cc_start: 0.6492 (tttt) cc_final: 0.6197 (ttpp) REVERT: A 482 ARG cc_start: 0.5195 (mmm-85) cc_final: 0.4975 (mmm-85) REVERT: A 527 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.5318 (tt0) REVERT: A 585 LEU cc_start: 0.6331 (mt) cc_final: 0.6130 (mm) REVERT: B 357 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7418 (ttt-90) REVERT: B 378 LYS cc_start: 0.6408 (mmtt) cc_final: 0.5799 (tptp) REVERT: B 462 LYS cc_start: 0.6851 (mmtp) cc_final: 0.6622 (mppt) REVERT: B 468 ILE cc_start: 0.8254 (mt) cc_final: 0.7877 (mm) outliers start: 16 outliers final: 9 residues processed: 94 average time/residue: 1.2282 time to fit residues: 121.9543 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 : 0.764 ------------------------------------------------------------------------------- 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 450 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 0.0470 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN A 524 GLN B 388 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6821 Z= 0.176 Angle : 0.533 7.571 9271 Z= 0.272 Chirality : 0.044 0.335 1014 Planarity : 0.003 0.028 1175 Dihedral : 7.970 72.238 1185 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.17 % Allowed : 13.69 % Favored : 83.14 % 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: 1.23 (0.31), residues: 786 helix: 2.14 (0.27), residues: 392 sheet: 0.78 (0.70), residues: 52 loop : -0.78 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS A 34 PHE 0.013 0.001 PHE B 347 TYR 0.014 0.001 TYR A 385 ARG 0.002 0.000 ARG B 346 *********************** 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 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6334 (mt-10) cc_final: 0.5905 (mt-10) REVERT: A 81 GLN cc_start: 0.8166 (mt0) cc_final: 0.7306 (mm110) REVERT: A 131 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6282 (ttmt) REVERT: A 190 MET cc_start: 0.5427 (tmm) cc_final: 0.4716 (tmm) REVERT: A 224 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.6070 (mm-30) REVERT: A 231 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6555 (mt-10) REVERT: A 295 ASP cc_start: 0.5531 (m-30) cc_final: 0.5223 (m-30) REVERT: A 441 LYS cc_start: 0.6501 (tttt) cc_final: 0.6200 (ttpp) REVERT: A 527 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.5191 (tt0) REVERT: A 546 ASN cc_start: 0.6474 (m110) cc_final: 0.5414 (p0) REVERT: A 571 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6444 (tt0) REVERT: A 585 LEU cc_start: 0.6284 (mt) cc_final: 0.6062 (mm) REVERT: B 354 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7613 (t0) REVERT: B 378 LYS cc_start: 0.6406 (mmtt) cc_final: 0.5810 (tptp) REVERT: B 440 LYS cc_start: 0.7922 (ttpp) cc_final: 0.7162 (mmtm) REVERT: B 468 ILE cc_start: 0.8239 (mt) cc_final: 0.7832 (mm) outliers start: 22 outliers final: 9 residues processed: 101 average time/residue: 1.1831 time to fit residues: 126.2412 Evaluate side-chains 94 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 367 ASP Chi-restraints excluded: chain A residue 450 LEU 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 B residue 354 ASN Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 B 422 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6821 Z= 0.244 Angle : 0.578 8.148 9271 Z= 0.298 Chirality : 0.046 0.343 1014 Planarity : 0.004 0.037 1175 Dihedral : 7.743 71.470 1185 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.75 % Allowed : 13.54 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.30), residues: 786 helix: 1.97 (0.27), residues: 392 sheet: 0.75 (0.70), residues: 52 loop : -0.92 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.004 0.001 HIS A 540 PHE 0.018 0.002 PHE B 347 TYR 0.019 0.002 TYR A 385 ARG 0.003 0.001 ARG B 466 *********************** 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 110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6342 (mt-10) cc_final: 0.5940 (mt-10) REVERT: A 81 GLN cc_start: 0.8331 (mt0) cc_final: 0.7549 (mm110) REVERT: A 131 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6337 (ttmt) REVERT: A 190 MET cc_start: 0.5412 (tmm) cc_final: 0.4742 (tmm) REVERT: A 231 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6550 (mt-10) REVERT: A 295 ASP cc_start: 0.5588 (m-30) cc_final: 0.5283 (m-30) REVERT: A 441 LYS cc_start: 0.6510 (tttt) cc_final: 0.6190 (ttpp) REVERT: A 527 GLU cc_start: 0.5755 (OUTLIER) cc_final: 0.5322 (tt0) REVERT: A 546 ASN cc_start: 0.6806 (m110) cc_final: 0.5592 (p0) REVERT: B 354 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7564 (t0) REVERT: B 378 LYS cc_start: 0.6271 (mmtt) cc_final: 0.5719 (tmtt) REVERT: B 468 ILE cc_start: 0.8149 (mt) cc_final: 0.7684 (mm) outliers start: 26 outliers final: 13 residues processed: 100 average time/residue: 1.0867 time to fit residues: 115.1932 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 : 0.739 ------------------------------------------------------------------------------- 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 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 431 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 A residue 574 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.0770 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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 B 417 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6821 Z= 0.183 Angle : 0.537 7.464 9271 Z= 0.275 Chirality : 0.044 0.331 1014 Planarity : 0.003 0.027 1175 Dihedral : 7.365 68.510 1185 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.03 % Allowed : 14.84 % 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: 1.16 (0.31), residues: 786 helix: 2.10 (0.27), residues: 392 sheet: 0.90 (0.71), residues: 52 loop : -0.88 (0.32), residues: 342 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 A 315 TYR 0.013 0.001 TYR A 385 ARG 0.003 0.000 ARG A 482 *********************** 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 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6291 (mt-10) cc_final: 0.5899 (mt-10) REVERT: A 81 GLN cc_start: 0.8338 (mt0) cc_final: 0.7550 (mm110) REVERT: A 131 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6289 (ttmt) REVERT: A 156 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6721 (tt) REVERT: A 190 MET cc_start: 0.5394 (tmm) cc_final: 0.4659 (tmm) REVERT: A 231 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6557 (mt-10) REVERT: A 295 ASP cc_start: 0.5574 (m-30) cc_final: 0.5266 (m-30) REVERT: A 441 LYS cc_start: 0.6483 (tttt) cc_final: 0.6157 (ttpp) REVERT: A 527 GLU cc_start: 0.5596 (OUTLIER) cc_final: 0.5092 (tt0) REVERT: A 546 ASN cc_start: 0.6690 (m110) cc_final: 0.5514 (p0) REVERT: B 354 ASN cc_start: 0.7868 (OUTLIER) cc_final: 0.7534 (t0) REVERT: B 378 LYS cc_start: 0.6260 (mmtt) cc_final: 0.5661 (tmtt) REVERT: B 440 LYS cc_start: 0.7907 (ttpp) cc_final: 0.7059 (mmtm) REVERT: B 468 ILE cc_start: 0.8136 (mt) cc_final: 0.7681 (mm) outliers start: 21 outliers final: 13 residues processed: 94 average time/residue: 1.1269 time to fit residues: 112.1890 Evaluate side-chains 96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 376 MET Chi-restraints excluded: chain A residue 431 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 354 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 516 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.0370 chunk 22 optimal weight: 0.6980 overall best weight: 0.8662 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6821 Z= 0.203 Angle : 0.549 7.236 9271 Z= 0.282 Chirality : 0.044 0.327 1014 Planarity : 0.003 0.028 1175 Dihedral : 7.206 66.327 1185 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.03 % Allowed : 15.27 % Favored : 81.70 % 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: 2.06 (0.27), residues: 394 sheet: 0.97 (0.71), residues: 52 loop : -0.88 (0.33), residues: 340 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 0.015 0.001 TYR A 385 ARG 0.003 0.000 ARG B 466 *********************** 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 107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6200 (mt-10) cc_final: 0.5798 (mt-10) REVERT: A 81 GLN cc_start: 0.8348 (mt0) cc_final: 0.7565 (mm110) REVERT: A 131 LYS cc_start: 0.6731 (OUTLIER) cc_final: 0.6280 (ttmt) REVERT: A 190 MET cc_start: 0.5383 (tmm) cc_final: 0.4650 (tmm) REVERT: A 231 GLU cc_start: 0.6764 (mm-30) cc_final: 0.6533 (mt-10) REVERT: A 295 ASP cc_start: 0.5528 (m-30) cc_final: 0.5184 (m-30) REVERT: A 441 LYS cc_start: 0.6498 (tttt) cc_final: 0.6163 (ttpp) REVERT: A 527 GLU cc_start: 0.5609 (OUTLIER) cc_final: 0.5132 (tt0) REVERT: A 546 ASN cc_start: 0.6727 (m110) cc_final: 0.5522 (p0) REVERT: B 354 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.7646 (t0) REVERT: B 378 LYS cc_start: 0.6280 (mmtt) cc_final: 0.5726 (tmtt) REVERT: B 468 ILE cc_start: 0.8136 (mt) cc_final: 0.7678 (mm) outliers start: 21 outliers final: 14 residues processed: 97 average time/residue: 1.1191 time to fit residues: 114.9689 Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 431 ASP 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 574 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 516 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 68 optimal weight: 0.0770 chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6821 Z= 0.200 Angle : 0.556 7.825 9271 Z= 0.283 Chirality : 0.044 0.323 1014 Planarity : 0.003 0.027 1175 Dihedral : 7.107 64.864 1185 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.31 % Allowed : 15.27 % 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: 1.08 (0.30), residues: 786 helix: 1.98 (0.27), residues: 394 sheet: 0.98 (0.71), residues: 52 loop : -0.88 (0.33), residues: 340 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 0.014 0.001 TYR A 385 ARG 0.003 0.000 ARG A 482 *********************** 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: 23 poor density : 82 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6198 (mt-10) cc_final: 0.5795 (mt-10) REVERT: A 81 GLN cc_start: 0.8334 (mt0) cc_final: 0.7578 (mm110) REVERT: A 131 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6277 (ttmt) REVERT: A 190 MET cc_start: 0.5383 (tmm) cc_final: 0.4650 (tmm) REVERT: A 231 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6530 (mt-10) REVERT: A 295 ASP cc_start: 0.5508 (m-30) cc_final: 0.5181 (m-30) REVERT: A 401 HIS cc_start: 0.6628 (OUTLIER) cc_final: 0.5528 (m-70) REVERT: A 441 LYS cc_start: 0.6533 (tttt) cc_final: 0.6155 (ttpp) REVERT: A 527 GLU cc_start: 0.5605 (OUTLIER) cc_final: 0.5129 (tt0) REVERT: B 354 ASN cc_start: 0.7979 (OUTLIER) cc_final: 0.7659 (t0) REVERT: B 378 LYS cc_start: 0.6279 (mmtt) cc_final: 0.5726 (tmtt) REVERT: B 440 LYS cc_start: 0.7797 (ttpp) cc_final: 0.6920 (mmtm) REVERT: B 468 ILE cc_start: 0.8140 (mt) cc_final: 0.7682 (mm) outliers start: 23 outliers final: 16 residues processed: 96 average time/residue: 1.0984 time to fit residues: 111.7085 Evaluate side-chains 99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 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 431 ASP Chi-restraints excluded: chain A residue 450 LEU 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 354 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 516 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 0.0070 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 0.0770 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6821 Z= 0.146 Angle : 0.536 7.366 9271 Z= 0.269 Chirality : 0.043 0.314 1014 Planarity : 0.003 0.028 1175 Dihedral : 6.782 60.886 1185 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.16 % Allowed : 17.15 % Favored : 80.69 % 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: 1.26 (0.31), residues: 786 helix: 2.09 (0.27), residues: 399 sheet: 1.07 (0.71), residues: 52 loop : -0.79 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.002 0.001 HIS A 540 PHE 0.009 0.001 PHE A 327 TYR 0.009 0.001 TYR A 385 ARG 0.002 0.000 ARG A 482 *********************** 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 100 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6292 (mt-10) cc_final: 0.5894 (mt-10) REVERT: A 81 GLN cc_start: 0.8289 (mt0) cc_final: 0.7548 (mm110) REVERT: A 131 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6257 (ttmt) REVERT: A 190 MET cc_start: 0.5411 (tmm) cc_final: 0.4697 (tmm) REVERT: A 231 GLU cc_start: 0.6753 (mm-30) cc_final: 0.6522 (mt-10) REVERT: A 295 ASP cc_start: 0.5576 (m-30) cc_final: 0.5246 (m-30) REVERT: A 441 LYS cc_start: 0.6488 (tttt) cc_final: 0.6118 (ttpp) REVERT: A 546 ASN cc_start: 0.6098 (m110) cc_final: 0.5294 (p0) REVERT: A 585 LEU cc_start: 0.6308 (mt) cc_final: 0.6063 (mm) REVERT: B 378 LYS cc_start: 0.6277 (mmtt) cc_final: 0.5699 (tmtt) REVERT: B 440 LYS cc_start: 0.7792 (ttpp) cc_final: 0.6923 (mmtm) REVERT: B 468 ILE cc_start: 0.8130 (mt) cc_final: 0.7681 (mm) outliers start: 15 outliers final: 7 residues processed: 90 average time/residue: 1.1613 time to fit residues: 110.6876 Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 131 LYS 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 543 ASP Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6821 Z= 0.168 Angle : 0.540 7.321 9271 Z= 0.272 Chirality : 0.043 0.304 1014 Planarity : 0.003 0.028 1175 Dihedral : 6.576 57.796 1185 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.30 % Allowed : 18.44 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.30), residues: 786 helix: 2.09 (0.27), residues: 395 sheet: 1.10 (0.71), residues: 52 loop : -0.83 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS A 540 PHE 0.010 0.001 PHE A 315 TYR 0.012 0.001 TYR A 385 ARG 0.002 0.000 ARG A 559 ********************** 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 96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6308 (mt-10) cc_final: 0.5917 (mt-10) REVERT: A 81 GLN cc_start: 0.8274 (mt0) cc_final: 0.7570 (mm-40) REVERT: A 131 LYS cc_start: 0.6761 (OUTLIER) cc_final: 0.6155 (ttmt) REVERT: A 190 MET cc_start: 0.5406 (tmm) cc_final: 0.4644 (tmm) REVERT: A 231 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6522 (mt-10) REVERT: A 295 ASP cc_start: 0.5479 (m-30) cc_final: 0.5145 (m-30) REVERT: A 441 LYS cc_start: 0.6462 (tttt) cc_final: 0.6092 (ttpp) REVERT: A 546 ASN cc_start: 0.5763 (m110) cc_final: 0.5110 (p0) REVERT: A 585 LEU cc_start: 0.6296 (mt) cc_final: 0.6066 (mm) REVERT: B 378 LYS cc_start: 0.6267 (mmtt) cc_final: 0.5723 (tmtt) REVERT: B 388 ASN cc_start: 0.7243 (m-40) cc_final: 0.6476 (t0) REVERT: B 440 LYS cc_start: 0.7609 (ttpp) cc_final: 0.6704 (mmtm) REVERT: B 468 ILE cc_start: 0.8139 (mt) cc_final: 0.7704 (mm) outliers start: 9 outliers final: 6 residues processed: 91 average time/residue: 1.2033 time to fit residues: 115.6852 Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS 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 543 ASP Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.162987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.130861 restraints weight = 7790.623| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.16 r_work: 0.3231 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6821 Z= 0.194 Angle : 0.557 7.296 9271 Z= 0.282 Chirality : 0.044 0.309 1014 Planarity : 0.003 0.027 1175 Dihedral : 6.561 55.314 1185 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.30 % Allowed : 18.30 % 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: 1.17 (0.30), residues: 786 helix: 2.03 (0.27), residues: 394 sheet: 1.13 (0.71), residues: 52 loop : -0.82 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS A 540 PHE 0.011 0.001 PHE B 371 TYR 0.014 0.001 TYR A 385 ARG 0.002 0.000 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2867.86 seconds wall clock time: 82 minutes 34.98 seconds (4954.98 seconds total)