Starting phenix.real_space_refine on Fri Jan 17 10:39:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xv0_38688/01_2025/8xv0_38688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xv0_38688/01_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_38688/01_2025/8xv0_38688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xv0_38688/01_2025/8xv0_38688.map" model { file = "/net/cci-nas-00/data/ceres_data/8xv0_38688/01_2025/8xv0_38688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xv0_38688/01_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-5571/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: 5.24, per 1000 atoms: 0.79 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: 1.72 Conformation dependent library (CDL) restraints added in 898.3 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: 0.75 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: 1.87 Time building geometry restraints manager: 1.98 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.300 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.520 ------------------------------------------------------------------------------- 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 : 0.687 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: 1.2884 time to fit residues: 202.6347 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 : 0.736 ------------------------------------------------------------------------------- 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 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 : 0.718 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: 1.2467 time to fit residues: 139.1147 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 6821 Z= 0.276 Angle : 0.606 7.123 9271 Z= 0.311 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 *********************** 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 : 0.754 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: 1.1897 time to fit residues: 118.4222 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 : 0.769 ------------------------------------------------------------------------------- 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: 5.9990 chunk 69 optimal weight: 0.0010 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: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN 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 = 0.3799 r_free = 0.3799 target = 0.161684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129348 restraints weight = 7920.317| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.13 r_work: 0.3248 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6821 Z= 0.242 Angle : 0.593 7.499 9271 Z= 0.303 Chirality : 0.047 0.355 1014 Planarity : 0.004 0.033 1175 Dihedral : 8.712 75.156 1185 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.18 % Allowed : 13.69 % 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: 0.98 (0.30), residues: 786 helix: 1.83 (0.27), residues: 399 sheet: 0.68 (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 0.003 0.001 ARG B 457 *********************** 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: 29 poor density : 78 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7599 (mt-10) REVERT: A 81 GLN cc_start: 0.8393 (mt0) cc_final: 0.8056 (mm110) REVERT: A 131 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7275 (ttmt) REVERT: A 156 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7363 (tt) REVERT: A 190 MET cc_start: 0.7161 (tmm) cc_final: 0.6297 (tmm) REVERT: A 295 ASP cc_start: 0.7083 (m-30) cc_final: 0.6733 (m-30) REVERT: A 401 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.7617 (m-70) REVERT: A 527 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: A 546 ASN cc_start: 0.7320 (m110) cc_final: 0.6249 (p0) REVERT: A 579 MET cc_start: 0.7895 (mtm) cc_final: 0.7562 (mtm) REVERT: A 600 LYS cc_start: 0.7732 (pttm) cc_final: 0.7402 (pttt) REVERT: B 378 LYS cc_start: 0.7496 (mmtt) cc_final: 0.7230 (tptp) REVERT: B 417 ASN cc_start: 0.7966 (t160) cc_final: 0.7730 (t0) REVERT: B 440 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8160 (mptt) REVERT: B 462 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7542 (mtpt) outliers start: 29 outliers final: 14 residues processed: 96 average time/residue: 1.0579 time to fit residues: 107.9915 Evaluate side-chains 96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 61 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 0.0770 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.0040 chunk 16 optimal weight: 0.9980 overall best weight: 0.5550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 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 = 0.3816 r_free = 0.3816 target = 0.163325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131544 restraints weight = 7917.065| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.12 r_work: 0.3241 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6821 Z= 0.155 Angle : 0.515 7.060 9271 Z= 0.263 Chirality : 0.043 0.311 1014 Planarity : 0.003 0.029 1175 Dihedral : 7.612 70.763 1185 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.60 % Allowed : 13.98 % Favored : 82.42 % 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: 1.22 (0.31), residues: 786 helix: 2.05 (0.27), residues: 399 sheet: 0.89 (0.70), residues: 52 loop : -0.76 (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 315 TYR 0.010 0.001 TYR A 385 ARG 0.004 0.000 ARG A 482 *********************** 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 : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7434 (mt-10) REVERT: A 81 GLN cc_start: 0.8485 (mt0) cc_final: 0.8159 (mm-40) REVERT: A 131 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7238 (ttmt) REVERT: A 190 MET cc_start: 0.7167 (tmm) cc_final: 0.6335 (tmm) REVERT: A 224 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7014 (mm-30) REVERT: A 295 ASP cc_start: 0.7084 (m-30) cc_final: 0.6723 (m-30) REVERT: A 401 HIS cc_start: 0.7983 (OUTLIER) cc_final: 0.7528 (m-70) REVERT: A 546 ASN cc_start: 0.7178 (m110) cc_final: 0.6212 (p0) REVERT: A 571 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: A 579 MET cc_start: 0.7704 (mtm) cc_final: 0.7367 (mtm) REVERT: B 417 ASN cc_start: 0.7886 (t160) cc_final: 0.7639 (t0) REVERT: B 462 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7407 (mtpt) outliers start: 25 outliers final: 9 residues processed: 100 average time/residue: 1.1259 time to fit residues: 119.3009 Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 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 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 401 HIS 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: 1.9990 chunk 66 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.162775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130603 restraints weight = 7825.831| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.19 r_work: 0.3279 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 0.030 6821 Z= 0.193 Angle : 0.549 6.446 9271 Z= 0.280 Chirality : 0.044 0.332 1014 Planarity : 0.003 0.029 1175 Dihedral : 7.360 68.929 1185 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.03 % Allowed : 15.42 % Favored : 81.56 % 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: 1.98 (0.27), residues: 399 sheet: 0.93 (0.71), residues: 52 loop : -0.80 (0.33), residues: 335 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 0.011 0.001 PHE A 315 TYR 0.015 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 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7399 (mt-10) REVERT: A 81 GLN cc_start: 0.8514 (mt0) cc_final: 0.8163 (mm110) REVERT: A 131 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7223 (ttmt) REVERT: A 156 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7290 (tt) REVERT: A 190 MET cc_start: 0.7157 (tmm) cc_final: 0.6317 (tmm) REVERT: A 224 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7073 (mm-30) REVERT: A 295 ASP cc_start: 0.7083 (m-30) cc_final: 0.6718 (m-30) REVERT: A 546 ASN cc_start: 0.7222 (m110) cc_final: 0.6253 (p0) REVERT: A 579 MET cc_start: 0.7851 (mtm) cc_final: 0.7597 (mtm) REVERT: B 417 ASN cc_start: 0.7942 (t160) cc_final: 0.7706 (t0) REVERT: B 440 LYS cc_start: 0.8656 (ttpp) cc_final: 0.8135 (mptt) REVERT: B 462 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7456 (mtpt) outliers start: 21 outliers final: 11 residues processed: 93 average time/residue: 1.0884 time to fit residues: 107.7239 Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 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 543 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 462 LYS 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 14 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.162544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130308 restraints weight = 7850.427| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.20 r_work: 0.3235 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2874 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= 0.194 Angle : 0.543 6.327 9271 Z= 0.279 Chirality : 0.044 0.329 1014 Planarity : 0.003 0.029 1175 Dihedral : 7.168 66.217 1185 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.17 % Allowed : 15.85 % Favored : 80.98 % 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: 1.13 (0.31), residues: 786 helix: 2.03 (0.27), residues: 394 sheet: 0.86 (0.70), residues: 52 loop : -0.84 (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 0.014 0.001 PHE B 371 TYR 0.014 0.001 TYR A 385 ARG 0.002 0.000 ARG A 482 *********************** 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 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7374 (mt-10) REVERT: A 81 GLN cc_start: 0.8553 (mt0) cc_final: 0.8178 (mm-40) REVERT: A 131 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7170 (ttmt) REVERT: A 190 MET cc_start: 0.7135 (tmm) cc_final: 0.6262 (tmm) REVERT: A 224 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7063 (mm-30) REVERT: A 295 ASP cc_start: 0.7032 (m-30) cc_final: 0.6663 (m-30) REVERT: A 401 HIS cc_start: 0.8242 (OUTLIER) cc_final: 0.7568 (m-70) REVERT: A 527 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: A 546 ASN cc_start: 0.7231 (m110) cc_final: 0.6280 (p0) REVERT: A 571 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: A 579 MET cc_start: 0.7799 (mtm) cc_final: 0.7463 (mtm) REVERT: B 417 ASN cc_start: 0.7922 (t160) cc_final: 0.7680 (t0) REVERT: B 462 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7479 (mtpt) outliers start: 22 outliers final: 11 residues processed: 93 average time/residue: 1.1853 time to fit residues: 116.5070 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 : 0.752 ------------------------------------------------------------------------------- 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 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 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 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 38 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.161705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129848 restraints weight = 7916.799| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.14 r_work: 0.3207 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2988 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= 0.210 Angle : 0.558 6.260 9271 Z= 0.286 Chirality : 0.044 0.329 1014 Planarity : 0.004 0.030 1175 Dihedral : 7.128 65.010 1185 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.03 % Allowed : 16.43 % Favored : 80.55 % 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: 1.00 (0.30), residues: 786 helix: 1.88 (0.27), residues: 395 sheet: 0.82 (0.68), residues: 54 loop : -0.86 (0.33), residues: 337 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 0.012 0.001 PHE B 371 TYR 0.015 0.001 TYR A 385 ARG 0.002 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 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7463 (mt-10) REVERT: A 81 GLN cc_start: 0.8549 (mt0) cc_final: 0.8162 (mm110) REVERT: A 82 MET cc_start: 0.8302 (mtm) cc_final: 0.8099 (mtp) REVERT: A 131 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7063 (ttmt) REVERT: A 156 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7246 (tt) REVERT: A 190 MET cc_start: 0.6987 (tmm) cc_final: 0.6082 (tmm) REVERT: A 295 ASP cc_start: 0.7045 (m-30) cc_final: 0.6646 (m-30) REVERT: A 401 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7597 (m-70) REVERT: A 527 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: A 579 MET cc_start: 0.7847 (mtm) cc_final: 0.7544 (mtm) REVERT: B 417 ASN cc_start: 0.7913 (t160) cc_final: 0.7688 (t0) REVERT: B 440 LYS cc_start: 0.8627 (ttpp) cc_final: 0.8106 (mmtm) REVERT: B 462 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7470 (mtpt) outliers start: 21 outliers final: 11 residues processed: 95 average time/residue: 1.2334 time to fit residues: 124.3353 Evaluate side-chains 95 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 24 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 0.0270 chunk 11 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 0.0020 chunk 55 optimal weight: 0.1980 overall best weight: 0.3446 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.165379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133705 restraints weight = 7889.203| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.14 r_work: 0.3266 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6821 Z= 0.142 Angle : 0.524 7.162 9271 Z= 0.264 Chirality : 0.042 0.313 1014 Planarity : 0.003 0.028 1175 Dihedral : 6.716 59.953 1185 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.59 % Allowed : 17.44 % Favored : 79.97 % 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 (0.30), residues: 786 helix: 2.00 (0.27), residues: 402 sheet: 0.97 (0.70), residues: 52 loop : -0.71 (0.33), residues: 332 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 0.010 0.001 PHE A 327 TYR 0.008 0.001 TYR B 494 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 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7304 (mt-10) REVERT: A 75 GLU cc_start: 0.8151 (pt0) cc_final: 0.7835 (pt0) REVERT: A 81 GLN cc_start: 0.8466 (mt0) cc_final: 0.8159 (mm-40) REVERT: A 114 LYS cc_start: 0.8276 (pptt) cc_final: 0.8066 (pptt) REVERT: A 131 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7029 (ttmt) REVERT: A 156 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7231 (tt) REVERT: A 190 MET cc_start: 0.7180 (tmm) cc_final: 0.6359 (tmm) REVERT: A 224 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6999 (mm-30) REVERT: A 295 ASP cc_start: 0.7187 (m-30) cc_final: 0.6823 (m-30) REVERT: A 401 HIS cc_start: 0.8138 (OUTLIER) cc_final: 0.7854 (m-70) REVERT: A 546 ASN cc_start: 0.6272 (m110) cc_final: 0.5697 (p0) REVERT: A 571 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: A 579 MET cc_start: 0.7630 (mtm) cc_final: 0.7329 (mtm) REVERT: B 388 ASN cc_start: 0.7343 (m-40) cc_final: 0.6894 (t0) REVERT: B 440 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8123 (mmtm) REVERT: B 462 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7387 (mtpt) outliers start: 18 outliers final: 8 residues processed: 96 average time/residue: 1.2139 time to fit residues: 123.1026 Evaluate side-chains 96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 34 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 0.0270 chunk 59 optimal weight: 0.0370 chunk 6 optimal weight: 0.0870 overall best weight: 0.3294 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.166614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.135541 restraints weight = 7972.839| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.09 r_work: 0.3275 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6821 Z= 0.137 Angle : 0.514 6.938 9271 Z= 0.258 Chirality : 0.042 0.299 1014 Planarity : 0.003 0.028 1175 Dihedral : 6.119 52.045 1185 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.59 % Allowed : 19.16 % Favored : 79.25 % 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: 1.27 (0.30), residues: 786 helix: 2.05 (0.27), residues: 402 sheet: 1.65 (0.79), residues: 42 loop : -0.76 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.002 0.000 HIS A 540 PHE 0.009 0.001 PHE A 315 TYR 0.008 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 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8398 (mt0) cc_final: 0.8168 (mm-40) REVERT: A 131 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7065 (ttmt) REVERT: A 156 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7171 (tt) REVERT: A 190 MET cc_start: 0.7160 (tmm) cc_final: 0.6219 (tmm) REVERT: A 295 ASP cc_start: 0.7138 (m-30) cc_final: 0.6829 (m-30) REVERT: A 401 HIS cc_start: 0.7940 (OUTLIER) cc_final: 0.7678 (m-70) REVERT: A 546 ASN cc_start: 0.6276 (m110) cc_final: 0.5747 (p0) REVERT: A 579 MET cc_start: 0.7580 (mtm) cc_final: 0.7322 (mtm) REVERT: B 378 LYS cc_start: 0.7768 (mmmt) cc_final: 0.7325 (tmtt) REVERT: B 388 ASN cc_start: 0.7244 (m-40) cc_final: 0.7030 (t0) REVERT: B 417 ASN cc_start: 0.7801 (t160) cc_final: 0.7541 (t0) REVERT: B 440 LYS cc_start: 0.8566 (ttpp) cc_final: 0.8101 (mptt) REVERT: B 462 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7340 (mtpt) outliers start: 11 outliers final: 7 residues processed: 99 average time/residue: 1.1381 time to fit residues: 119.1992 Evaluate side-chains 93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 156 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 332 MET 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 543 ASP 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: 0.9980 chunk 19 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 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 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.163463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131707 restraints weight = 7905.880| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.11 r_work: 0.3240 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6821 Z= 0.202 Angle : 0.572 7.130 9271 Z= 0.289 Chirality : 0.044 0.287 1014 Planarity : 0.004 0.029 1175 Dihedral : 6.251 49.984 1185 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.73 % Allowed : 19.31 % Favored : 78.96 % 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 (0.30), residues: 786 helix: 1.92 (0.27), residues: 403 sheet: 0.96 (0.70), residues: 52 loop : -0.76 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS A 540 PHE 0.010 0.001 PHE B 371 TYR 0.015 0.001 TYR A 385 ARG 0.002 0.000 ARG A 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5051.92 seconds wall clock time: 91 minutes 13.93 seconds (5473.93 seconds total)