Starting phenix.real_space_refine on Sun Aug 4 13:11:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn3_38496/08_2024/8xn3_38496.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn3_38496/08_2024/8xn3_38496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn3_38496/08_2024/8xn3_38496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn3_38496/08_2024/8xn3_38496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn3_38496/08_2024/8xn3_38496.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn3_38496/08_2024/8xn3_38496.cif" } resolution = 2.64 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= 0.009 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 4872 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4161 2.51 5 N 1076 2.21 5 O 1230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 498": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6505 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4872 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} bond proxies already assigned to first conformer: 4987 Chain: "B" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1548 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 34 " occ=0.63 ... (18 atoms not shown) pdb=" NE2BHIS A 34 " occ=0.37 Time building chain proxies: 8.70, per 1000 atoms: 1.34 Number of scatterers: 6505 At special positions: 0 Unit cell: (97.768, 69.488, 121.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1230 8.00 N 1076 7.00 C 4161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 103 " " NAG A 704 " - " ASN A 432 " " NAG A 705 " - " ASN A 546 " " NAG A 706 " - " ASN A 322 " Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 707 " pdb="ZN ZN A 707 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 707 " - pdb=" NE2 HIS A 374 " 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 6 sheets defined 54.6% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.668A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A 38 " --> pdb=" O AHIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.535A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 102 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 194 removed outlier: 4.182A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.779A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.761A 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 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.511A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.703A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.137A 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 485 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 509 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.429A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.842A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 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 337 through 342 removed outlier: 3.532A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.698A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 134 removed outlier: 3.573A pdb=" N ASN A 134 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU A 140 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.508A 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 352 removed outlier: 6.164A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.864A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (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 474 320 hydrogen bonds defined for protein. 931 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: 1.69 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1084 1.32 - 1.44: 1943 1.44 - 1.57: 3605 1.57 - 1.69: 0 1.69 - 1.82: 58 Bond restraints: 6690 Sorted by residual: bond pdb=" C PRO B 491 " pdb=" O PRO B 491 " ideal model delta sigma weight residual 1.238 1.195 0.043 1.22e-02 6.72e+03 1.25e+01 bond pdb=" CA SER B 490 " pdb=" CB SER B 490 " ideal model delta sigma weight residual 1.532 1.487 0.045 1.50e-02 4.44e+03 9.09e+00 bond pdb=" N PRO B 491 " pdb=" CA PRO B 491 " ideal model delta sigma weight residual 1.470 1.430 0.040 1.34e-02 5.57e+03 8.86e+00 bond pdb=" N CYS B 488 " pdb=" CA CYS B 488 " ideal model delta sigma weight residual 1.464 1.493 -0.029 1.25e-02 6.40e+03 5.51e+00 bond pdb=" N GLN A 42 " pdb=" CA GLN A 42 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.30e-02 5.92e+03 4.65e+00 ... (remaining 6685 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.96: 236 106.96 - 113.72: 3572 113.72 - 120.47: 2685 120.47 - 127.23: 2504 127.23 - 133.99: 100 Bond angle restraints: 9097 Sorted by residual: angle pdb=" N TYR B 489 " pdb=" CA TYR B 489 " pdb=" CB TYR B 489 " ideal model delta sigma weight residual 110.87 101.76 9.11 1.51e+00 4.39e-01 3.64e+01 angle pdb=" C ASN A 338 " pdb=" CA ASN A 338 " pdb=" CB ASN A 338 " ideal model delta sigma weight residual 117.23 110.19 7.04 1.36e+00 5.41e-01 2.68e+01 angle pdb=" CA ASN A 338 " pdb=" C ASN A 338 " pdb=" N VAL A 339 " ideal model delta sigma weight residual 119.98 116.73 3.25 8.50e-01 1.38e+00 1.46e+01 angle pdb=" C SER B 494 " pdb=" CA SER B 494 " pdb=" CB SER B 494 " ideal model delta sigma weight residual 109.51 115.06 -5.55 1.71e+00 3.42e-01 1.06e+01 angle pdb=" CA SER B 490 " pdb=" C SER B 490 " pdb=" O SER B 490 " ideal model delta sigma weight residual 120.63 117.31 3.32 1.03e+00 9.43e-01 1.04e+01 ... (remaining 9092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 3651 17.25 - 34.49: 309 34.49 - 51.74: 42 51.74 - 68.98: 20 68.98 - 86.23: 8 Dihedral angle restraints: 4030 sinusoidal: 1702 harmonic: 2328 Sorted by residual: 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 -139.98 53.98 1 1.00e+01 1.00e-02 3.95e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 145.63 -52.63 1 1.00e+01 1.00e-02 3.77e+01 dihedral pdb=" CA SER B 494 " pdb=" C SER B 494 " pdb=" N TYR B 495 " pdb=" CA TYR B 495 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 4027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 867 0.065 - 0.130: 96 0.130 - 0.195: 2 0.195 - 0.260: 1 0.260 - 0.325: 2 Chirality restraints: 968 Sorted by residual: chirality pdb=" C1 NAG A 706 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 706 " pdb=" O5 NAG A 706 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 432 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA GLN B 493 " pdb=" N GLN B 493 " pdb=" C GLN B 493 " pdb=" CB GLN B 493 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 965 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 498 " -0.200 9.50e-02 1.11e+02 8.97e-02 4.94e+00 pdb=" NE ARG B 498 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 498 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 498 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 498 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.028 5.00e-02 4.00e+02 4.16e-02 2.76e+00 pdb=" N PRO A 583 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 19 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C SER A 19 " -0.029 2.00e-02 2.50e+03 pdb=" O SER A 19 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 20 " 0.010 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 71 2.63 - 3.20: 5885 3.20 - 3.77: 10302 3.77 - 4.33: 14250 4.33 - 4.90: 23075 Nonbonded interactions: 53583 Sorted by model distance: nonbonded pdb=" CD GLU A 402 " pdb="ZN ZN A 707 " model vdw 2.067 2.460 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 707 " model vdw 2.095 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 707 " model vdw 2.096 2.230 nonbonded pdb=" ND2 ASN B 417 " pdb=" CD1 LEU B 455 " model vdw 2.211 3.540 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.263 3.040 ... (remaining 53578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 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: 14.670 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.090 Process input model: 28.370 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 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 0.045 6690 Z= 0.209 Angle : 0.575 9.114 9097 Z= 0.329 Chirality : 0.044 0.325 968 Planarity : 0.005 0.090 1172 Dihedral : 13.619 86.227 2515 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 1.25 (0.31), residues: 790 helix: 1.74 (0.26), residues: 401 sheet: 1.03 (0.74), residues: 48 loop : -0.27 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 566 HIS 0.013 0.002 HIS A 378 PHE 0.019 0.001 PHE A 400 TYR 0.020 0.001 TYR A 385 ARG 0.002 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.6241 (t80) cc_final: 0.5817 (t80) REVERT: A 61 ASN cc_start: 0.5958 (m110) cc_final: 0.5753 (m-40) REVERT: A 62 MET cc_start: 0.7491 (ttt) cc_final: 0.7180 (ttp) REVERT: A 64 ASN cc_start: 0.7660 (m-40) cc_final: 0.7332 (m110) REVERT: A 67 ASP cc_start: 0.7027 (m-30) cc_final: 0.6692 (m-30) REVERT: A 69 TRP cc_start: 0.7966 (t-100) cc_final: 0.7742 (t-100) REVERT: A 87 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6175 (mm-30) REVERT: A 160 GLU cc_start: 0.6808 (tt0) cc_final: 0.6366 (tm-30) REVERT: A 187 LYS cc_start: 0.6525 (mmmt) cc_final: 0.6072 (mmtp) REVERT: A 192 ARG cc_start: 0.7472 (mtt-85) cc_final: 0.7124 (mpp-170) REVERT: A 202 TYR cc_start: 0.7627 (t80) cc_final: 0.7306 (t80) REVERT: A 206 ASP cc_start: 0.7938 (t0) cc_final: 0.7541 (t0) REVERT: A 245 ARG cc_start: 0.6828 (ttp-170) cc_final: 0.6605 (ttp-170) REVERT: A 285 PHE cc_start: 0.6300 (m-80) cc_final: 0.6017 (m-10) REVERT: A 351 LEU cc_start: 0.8224 (mt) cc_final: 0.7764 (mp) REVERT: A 397 ASN cc_start: 0.7184 (p0) cc_final: 0.6917 (p0) REVERT: A 398 GLU cc_start: 0.7227 (pt0) cc_final: 0.6768 (pt0) REVERT: A 432 ASN cc_start: 0.5817 (m-40) cc_final: 0.5423 (p0) REVERT: A 455 MET cc_start: 0.7353 (tpt) cc_final: 0.7108 (tpp) REVERT: A 465 LYS cc_start: 0.7405 (mttp) cc_final: 0.7092 (mttp) REVERT: A 482 ARG cc_start: 0.6649 (ttm170) cc_final: 0.6444 (mtt180) REVERT: A 483 GLU cc_start: 0.6695 (tp30) cc_final: 0.6373 (tp30) REVERT: A 488 VAL cc_start: 0.7340 (p) cc_final: 0.6557 (t) REVERT: A 489 GLU cc_start: 0.6545 (pm20) cc_final: 0.5507 (pm20) REVERT: A 518 ARG cc_start: 0.6949 (ttp80) cc_final: 0.6309 (ttp80) REVERT: A 544 ILE cc_start: 0.7596 (pt) cc_final: 0.7343 (pp) REVERT: A 564 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6766 (mm-30) REVERT: A 594 TRP cc_start: 0.6045 (t60) cc_final: 0.5779 (t-100) REVERT: A 602 SER cc_start: 0.6763 (m) cc_final: 0.6122 (p) REVERT: A 610 TRP cc_start: 0.7239 (t60) cc_final: 0.6911 (t60) REVERT: A 613 TYR cc_start: 0.6606 (p90) cc_final: 0.6261 (p90) REVERT: B 396 TYR cc_start: 0.6643 (m-80) cc_final: 0.6016 (m-80) REVERT: B 409 GLN cc_start: 0.7880 (mt0) cc_final: 0.7504 (mt0) REVERT: B 453 TYR cc_start: 0.8016 (p90) cc_final: 0.7712 (p90) REVERT: B 462 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7527 (mmtp) REVERT: B 509 ARG cc_start: 0.7538 (mtt180) cc_final: 0.7263 (mtt180) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 1.0228 time to fit residues: 244.4166 Evaluate side-chains 200 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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: 0.6980 chunk 59 optimal weight: 0.4980 chunk 32 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.0270 chunk 37 optimal weight: 0.4980 chunk 45 optimal weight: 0.0970 chunk 70 optimal weight: 0.1980 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A A 194 ASN A 340 GLN A 345 HIS A 442 GLN A 535 HIS A 601 ASN B 354 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 505 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6690 Z= 0.207 Angle : 0.574 9.279 9097 Z= 0.298 Chirality : 0.048 0.367 968 Planarity : 0.005 0.041 1172 Dihedral : 5.730 54.365 987 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.16 % Allowed : 13.24 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.30), residues: 790 helix: 1.65 (0.26), residues: 401 sheet: 1.44 (0.80), residues: 48 loop : -0.47 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 302 HIS 0.007 0.002 HIS A 540 PHE 0.028 0.002 PHE A 369 TYR 0.015 0.001 TYR A 385 ARG 0.003 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 200 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.5696 (OUTLIER) cc_final: 0.5343 (mm) REVERT: A 50 TYR cc_start: 0.6226 (t80) cc_final: 0.5900 (t80) REVERT: A 62 MET cc_start: 0.7492 (ttt) cc_final: 0.7058 (ttp) REVERT: A 63 ASN cc_start: 0.7031 (m-40) cc_final: 0.6366 (m-40) REVERT: A 64 ASN cc_start: 0.7682 (m-40) cc_final: 0.7369 (m110) REVERT: A 67 ASP cc_start: 0.7046 (m-30) cc_final: 0.6711 (m-30) REVERT: A 86 GLN cc_start: 0.6848 (mp10) cc_final: 0.6429 (pm20) REVERT: A 98 GLN cc_start: 0.7470 (mm110) cc_final: 0.7007 (mm-40) REVERT: A 187 LYS cc_start: 0.6374 (mmmt) cc_final: 0.6069 (mmtp) REVERT: A 201 ASP cc_start: 0.7269 (t70) cc_final: 0.6214 (m-30) REVERT: A 202 TYR cc_start: 0.7680 (t80) cc_final: 0.7340 (t80) REVERT: A 206 ASP cc_start: 0.7795 (t0) cc_final: 0.7439 (t0) REVERT: A 256 ILE cc_start: 0.6432 (mp) cc_final: 0.6161 (mm) REVERT: A 291 ILE cc_start: 0.7451 (mt) cc_final: 0.7172 (mp) REVERT: A 302 TRP cc_start: 0.6587 (m-10) cc_final: 0.6364 (m-10) REVERT: A 351 LEU cc_start: 0.8285 (mt) cc_final: 0.8033 (mt) REVERT: A 364 VAL cc_start: 0.7856 (m) cc_final: 0.7614 (p) REVERT: A 421 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.7078 (mp) REVERT: A 472 GLN cc_start: 0.8016 (mt0) cc_final: 0.7312 (mp10) REVERT: A 475 LYS cc_start: 0.7347 (ttpt) cc_final: 0.7010 (ptmm) REVERT: A 482 ARG cc_start: 0.6745 (ttm170) cc_final: 0.6519 (mtt180) REVERT: A 483 GLU cc_start: 0.6657 (tp30) cc_final: 0.6323 (tp30) REVERT: A 488 VAL cc_start: 0.7543 (p) cc_final: 0.7065 (t) REVERT: A 514 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6133 (mtm-85) REVERT: A 518 ARG cc_start: 0.7026 (ttp80) cc_final: 0.6414 (ttp80) REVERT: A 564 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6861 (mm-30) REVERT: A 594 TRP cc_start: 0.6010 (t60) cc_final: 0.5796 (t-100) REVERT: A 600 LYS cc_start: 0.7609 (pttt) cc_final: 0.7248 (mtmm) REVERT: A 610 TRP cc_start: 0.7308 (t60) cc_final: 0.6945 (t60) REVERT: B 396 TYR cc_start: 0.6885 (m-80) cc_final: 0.6395 (m-80) REVERT: B 409 GLN cc_start: 0.7978 (mt0) cc_final: 0.7569 (mt0) REVERT: B 437 ASN cc_start: 0.8586 (m-40) cc_final: 0.8370 (m-40) REVERT: B 453 TYR cc_start: 0.7846 (p90) cc_final: 0.7501 (p90) REVERT: B 494 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7493 (t) REVERT: B 500 THR cc_start: 0.8166 (p) cc_final: 0.7825 (t) REVERT: B 509 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7111 (mtt180) outliers start: 15 outliers final: 7 residues processed: 205 average time/residue: 1.0473 time to fit residues: 226.5161 Evaluate side-chains 205 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 194 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 76 optimal weight: 0.0870 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A A 58 ASN A 61 ASN A 81 GLN A 96 GLN A 137 ASN A 239 HIS A 345 HIS B 360 ASN B 414 GLN B 448 ASN B 450 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 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 : 0.005 0.051 6690 Z= 0.336 Angle : 0.648 7.187 9097 Z= 0.341 Chirality : 0.052 0.393 968 Planarity : 0.005 0.045 1172 Dihedral : 5.834 45.320 987 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.45 % Allowed : 15.40 % Favored : 81.15 % 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: 0.67 (0.29), residues: 790 helix: 1.32 (0.25), residues: 400 sheet: 1.27 (0.76), residues: 49 loop : -0.73 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 302 HIS 0.009 0.002 HIS A 417 PHE 0.026 0.002 PHE A 369 TYR 0.019 0.002 TYR A 252 ARG 0.007 0.001 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 206 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.5598 (OUTLIER) cc_final: 0.5285 (mt) REVERT: A 26 LYS cc_start: 0.7080 (mttm) cc_final: 0.6824 (mttm) REVERT: A 50 TYR cc_start: 0.6339 (t80) cc_final: 0.5995 (t80) REVERT: A 62 MET cc_start: 0.7547 (ttt) cc_final: 0.7081 (ttp) REVERT: A 63 ASN cc_start: 0.6992 (m-40) cc_final: 0.6286 (m-40) REVERT: A 64 ASN cc_start: 0.7717 (m-40) cc_final: 0.7362 (m110) REVERT: A 67 ASP cc_start: 0.7072 (m-30) cc_final: 0.6717 (m-30) REVERT: A 74 LYS cc_start: 0.8193 (ttpt) cc_final: 0.7819 (ttpt) REVERT: A 87 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6750 (mm-30) REVERT: A 131 LYS cc_start: 0.6622 (pttm) cc_final: 0.6334 (ptmm) REVERT: A 150 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6754 (tm-30) REVERT: A 160 GLU cc_start: 0.6789 (tt0) cc_final: 0.6420 (tm-30) REVERT: A 187 LYS cc_start: 0.6234 (mmmt) cc_final: 0.5910 (mmtm) REVERT: A 192 ARG cc_start: 0.7479 (mtt-85) cc_final: 0.7054 (mpp-170) REVERT: A 201 ASP cc_start: 0.7292 (t70) cc_final: 0.6384 (m-30) REVERT: A 202 TYR cc_start: 0.7714 (t80) cc_final: 0.7305 (t80) REVERT: A 206 ASP cc_start: 0.7775 (t0) cc_final: 0.7262 (t0) REVERT: A 219 ARG cc_start: 0.7501 (mtm-85) cc_final: 0.7282 (mtt90) REVERT: A 267 LEU cc_start: 0.7533 (mt) cc_final: 0.7308 (mt) REVERT: A 291 ILE cc_start: 0.7509 (mt) cc_final: 0.7234 (mp) REVERT: A 302 TRP cc_start: 0.6669 (m-10) cc_final: 0.6147 (m-10) REVERT: A 310 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6374 (mp0) REVERT: A 351 LEU cc_start: 0.8374 (mt) cc_final: 0.8116 (mt) REVERT: A 455 MET cc_start: 0.7352 (tpt) cc_final: 0.6697 (tpt) REVERT: A 472 GLN cc_start: 0.8039 (mt0) cc_final: 0.7088 (mp10) REVERT: A 475 LYS cc_start: 0.7386 (ttpt) cc_final: 0.7060 (ttpt) REVERT: A 480 MET cc_start: 0.6072 (ttm) cc_final: 0.5683 (ttm) REVERT: A 482 ARG cc_start: 0.6943 (ttm170) cc_final: 0.6629 (mtt180) REVERT: A 483 GLU cc_start: 0.6640 (tp30) cc_final: 0.6308 (tp30) REVERT: A 488 VAL cc_start: 0.7729 (p) cc_final: 0.7196 (t) REVERT: A 508 ASN cc_start: 0.7555 (m110) cc_final: 0.7304 (m-40) REVERT: A 510 TYR cc_start: 0.7554 (m-80) cc_final: 0.7307 (m-10) REVERT: A 514 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.6427 (mtm-85) REVERT: A 518 ARG cc_start: 0.7021 (ttp80) cc_final: 0.6578 (ttp80) REVERT: A 539 LEU cc_start: 0.7911 (tp) cc_final: 0.7684 (tt) REVERT: A 564 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6958 (mm-30) REVERT: A 610 TRP cc_start: 0.7362 (t60) cc_final: 0.6897 (t60) REVERT: A 613 TYR cc_start: 0.6276 (p90) cc_final: 0.5688 (p90) REVERT: B 396 TYR cc_start: 0.7060 (m-80) cc_final: 0.6386 (m-80) REVERT: B 409 GLN cc_start: 0.7963 (mt0) cc_final: 0.7511 (mt0) REVERT: B 437 ASN cc_start: 0.8501 (m-40) cc_final: 0.8237 (m-40) REVERT: B 453 TYR cc_start: 0.7963 (p90) cc_final: 0.7598 (p90) REVERT: B 457 ARG cc_start: 0.6637 (ttt90) cc_final: 0.6194 (ttp-170) REVERT: B 500 THR cc_start: 0.8274 (p) cc_final: 0.7917 (t) REVERT: B 509 ARG cc_start: 0.7727 (mtt180) cc_final: 0.7275 (mtt180) outliers start: 24 outliers final: 9 residues processed: 217 average time/residue: 1.0829 time to fit residues: 247.2110 Evaluate side-chains 213 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 202 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 572 ASN 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: 0.0270 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 0.0970 chunk 37 optimal weight: 0.4980 chunk 67 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 GLN A 345 HIS B 448 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6690 Z= 0.283 Angle : 0.637 8.902 9097 Z= 0.331 Chirality : 0.050 0.378 968 Planarity : 0.005 0.046 1172 Dihedral : 5.516 43.480 987 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.45 % Allowed : 17.99 % Favored : 78.56 % 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: 0.64 (0.30), residues: 790 helix: 1.28 (0.26), residues: 397 sheet: 1.29 (0.76), residues: 49 loop : -0.70 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 477 HIS 0.005 0.002 HIS A 378 PHE 0.028 0.002 PHE A 369 TYR 0.024 0.002 TYR B 380 ARG 0.006 0.001 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 213 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.6970 (mttm) cc_final: 0.6695 (mttm) REVERT: A 50 TYR cc_start: 0.6310 (t80) cc_final: 0.6006 (t80) REVERT: A 57 GLU cc_start: 0.7428 (pm20) cc_final: 0.7093 (pm20) REVERT: A 61 ASN cc_start: 0.5972 (m-40) cc_final: 0.5596 (m110) REVERT: A 62 MET cc_start: 0.7529 (ttt) cc_final: 0.7082 (ttp) REVERT: A 63 ASN cc_start: 0.6990 (m-40) cc_final: 0.6307 (m-40) REVERT: A 64 ASN cc_start: 0.7731 (m-40) cc_final: 0.7370 (m110) REVERT: A 67 ASP cc_start: 0.7069 (m-30) cc_final: 0.6742 (m-30) REVERT: A 74 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7823 (ttpt) REVERT: A 87 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6655 (mm-30) REVERT: A 129 THR cc_start: 0.7572 (t) cc_final: 0.7362 (p) REVERT: A 131 LYS cc_start: 0.6650 (pttm) cc_final: 0.6357 (ptmm) REVERT: A 150 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6680 (tm-30) REVERT: A 192 ARG cc_start: 0.7420 (mtt-85) cc_final: 0.7007 (mpp-170) REVERT: A 201 ASP cc_start: 0.7269 (t70) cc_final: 0.6456 (m-30) REVERT: A 202 TYR cc_start: 0.7759 (t80) cc_final: 0.7419 (t80) REVERT: A 206 ASP cc_start: 0.7766 (t0) cc_final: 0.7324 (t0) REVERT: A 219 ARG cc_start: 0.7465 (mtm-85) cc_final: 0.7263 (mtt90) REVERT: A 291 ILE cc_start: 0.7520 (mt) cc_final: 0.7236 (mp) REVERT: A 302 TRP cc_start: 0.6599 (m-10) cc_final: 0.6215 (m-10) REVERT: A 310 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6427 (mp0) REVERT: A 351 LEU cc_start: 0.8369 (mt) cc_final: 0.8165 (mt) REVERT: A 366 MET cc_start: 0.6950 (ttm) cc_final: 0.6736 (ttp) REVERT: A 388 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7479 (mm-40) REVERT: A 408 MET cc_start: 0.7264 (tpp) cc_final: 0.7007 (ttp) REVERT: A 455 MET cc_start: 0.7399 (tpt) cc_final: 0.6791 (tpt) REVERT: A 472 GLN cc_start: 0.8048 (mt0) cc_final: 0.7257 (mp-120) REVERT: A 475 LYS cc_start: 0.7358 (ttpt) cc_final: 0.7033 (ttpt) REVERT: A 480 MET cc_start: 0.6110 (ttm) cc_final: 0.5679 (ttm) REVERT: A 482 ARG cc_start: 0.7012 (ttm170) cc_final: 0.6620 (mtt180) REVERT: A 483 GLU cc_start: 0.6651 (tp30) cc_final: 0.6321 (tp30) REVERT: A 488 VAL cc_start: 0.7723 (p) cc_final: 0.7082 (t) REVERT: A 508 ASN cc_start: 0.7428 (m110) cc_final: 0.7176 (m-40) REVERT: A 514 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6554 (mtm-85) REVERT: A 518 ARG cc_start: 0.6988 (ttp80) cc_final: 0.6496 (ttp80) REVERT: A 536 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7015 (mm-30) REVERT: A 539 LEU cc_start: 0.7958 (tp) cc_final: 0.7717 (tt) REVERT: A 564 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6946 (mm-30) REVERT: A 582 ARG cc_start: 0.6494 (mmm160) cc_final: 0.6151 (mmm160) REVERT: A 610 TRP cc_start: 0.7302 (t60) cc_final: 0.6861 (t60) REVERT: A 613 TYR cc_start: 0.6257 (p90) cc_final: 0.5697 (p90) REVERT: B 409 GLN cc_start: 0.7987 (mt0) cc_final: 0.7575 (mt0) REVERT: B 422 ASN cc_start: 0.7246 (m-40) cc_final: 0.6704 (m-40) REVERT: B 453 TYR cc_start: 0.7941 (p90) cc_final: 0.7505 (p90) REVERT: B 457 ARG cc_start: 0.6567 (ttt90) cc_final: 0.6143 (ttp-170) REVERT: B 500 THR cc_start: 0.8308 (p) cc_final: 0.7918 (t) REVERT: B 509 ARG cc_start: 0.7742 (mtt180) cc_final: 0.7076 (mtt180) outliers start: 24 outliers final: 10 residues processed: 224 average time/residue: 1.1563 time to fit residues: 271.7811 Evaluate side-chains 215 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 204 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain B residue 349 SER 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: 0.9990 chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 0.0970 chunk 19 optimal weight: 0.0020 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 96 GLN A 345 HIS A 522 GLN B 448 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 6690 Z= 0.326 Angle : 0.656 7.552 9097 Z= 0.343 Chirality : 0.052 0.391 968 Planarity : 0.005 0.049 1172 Dihedral : 5.506 42.024 987 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.60 % Allowed : 18.71 % Favored : 76.69 % 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: 0.49 (0.30), residues: 790 helix: 1.24 (0.26), residues: 395 sheet: 0.94 (0.73), residues: 49 loop : -0.82 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 566 HIS 0.006 0.002 HIS A 378 PHE 0.028 0.002 PHE A 369 TYR 0.027 0.002 TYR B 380 ARG 0.005 0.001 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 221 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7134 (mttm) cc_final: 0.6861 (mttm) REVERT: A 50 TYR cc_start: 0.6425 (t80) cc_final: 0.6134 (t80) REVERT: A 61 ASN cc_start: 0.5935 (m-40) cc_final: 0.5572 (m110) REVERT: A 62 MET cc_start: 0.7513 (ttt) cc_final: 0.7061 (ttp) REVERT: A 63 ASN cc_start: 0.6977 (m-40) cc_final: 0.6276 (m-40) REVERT: A 64 ASN cc_start: 0.7724 (m-40) cc_final: 0.7356 (m110) REVERT: A 67 ASP cc_start: 0.7089 (m-30) cc_final: 0.6730 (m-30) REVERT: A 72 PHE cc_start: 0.7717 (t80) cc_final: 0.7094 (t80) REVERT: A 74 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7830 (ttpt) REVERT: A 129 THR cc_start: 0.7648 (t) cc_final: 0.7375 (p) REVERT: A 131 LYS cc_start: 0.6626 (pttm) cc_final: 0.6341 (ptmm) REVERT: A 150 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6663 (tm-30) REVERT: A 160 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6465 (tm-30) REVERT: A 192 ARG cc_start: 0.7403 (mtt-85) cc_final: 0.7037 (mpp-170) REVERT: A 201 ASP cc_start: 0.7314 (t70) cc_final: 0.6568 (m-30) REVERT: A 202 TYR cc_start: 0.7804 (t80) cc_final: 0.7463 (t80) REVERT: A 206 ASP cc_start: 0.7746 (t0) cc_final: 0.7326 (t0) REVERT: A 267 LEU cc_start: 0.7560 (mt) cc_final: 0.7359 (mt) REVERT: A 285 PHE cc_start: 0.6891 (m-80) cc_final: 0.6414 (m-10) REVERT: A 302 TRP cc_start: 0.6583 (m-10) cc_final: 0.6252 (m-10) REVERT: A 307 ILE cc_start: 0.7845 (mt) cc_final: 0.7447 (mt) REVERT: A 310 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6437 (mp0) REVERT: A 366 MET cc_start: 0.6907 (ttm) cc_final: 0.6703 (ttp) REVERT: A 388 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7570 (mm-40) REVERT: A 455 MET cc_start: 0.7404 (tpt) cc_final: 0.6910 (tpt) REVERT: A 467 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6537 (mt-10) REVERT: A 470 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7188 (tppt) REVERT: A 475 LYS cc_start: 0.7354 (ttpt) cc_final: 0.7027 (ttpt) REVERT: A 480 MET cc_start: 0.6232 (ttm) cc_final: 0.5813 (ttm) REVERT: A 482 ARG cc_start: 0.6984 (ttm170) cc_final: 0.6586 (mtt180) REVERT: A 483 GLU cc_start: 0.6689 (tp30) cc_final: 0.6355 (tp30) REVERT: A 488 VAL cc_start: 0.7756 (p) cc_final: 0.7125 (t) REVERT: A 518 ARG cc_start: 0.7002 (ttp80) cc_final: 0.6559 (ttp80) REVERT: A 536 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7008 (tp30) REVERT: A 539 LEU cc_start: 0.8019 (tp) cc_final: 0.7788 (tt) REVERT: A 564 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6975 (mm-30) REVERT: A 582 ARG cc_start: 0.6547 (mmm160) cc_final: 0.6201 (mmm160) REVERT: A 610 TRP cc_start: 0.7322 (t60) cc_final: 0.6945 (t60) REVERT: A 613 TYR cc_start: 0.6434 (p90) cc_final: 0.5837 (p90) REVERT: B 409 GLN cc_start: 0.7991 (mt0) cc_final: 0.7576 (mt0) REVERT: B 422 ASN cc_start: 0.7246 (m-40) cc_final: 0.6734 (m-40) REVERT: B 453 TYR cc_start: 0.7990 (p90) cc_final: 0.7494 (p90) REVERT: B 457 ARG cc_start: 0.6547 (ttt90) cc_final: 0.6147 (ttp-170) REVERT: B 509 ARG cc_start: 0.7743 (mtt180) cc_final: 0.7170 (mtt180) outliers start: 32 outliers final: 15 residues processed: 233 average time/residue: 1.0988 time to fit residues: 269.4891 Evaluate side-chains 214 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 197 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.1980 chunk 18 optimal weight: 0.0870 chunk 75 optimal weight: 0.4980 chunk 62 optimal weight: 0.0980 chunk 34 optimal weight: 0.4980 chunk 6 optimal weight: 0.0470 chunk 24 optimal weight: 0.0980 chunk 39 optimal weight: 0.2980 chunk 72 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.1056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 81 GLN A 345 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN A 556 ASN B 448 ASN B 450 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6690 Z= 0.181 Angle : 0.607 9.194 9097 Z= 0.309 Chirality : 0.049 0.537 968 Planarity : 0.005 0.041 1172 Dihedral : 5.254 41.601 987 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.60 % Allowed : 21.87 % Favored : 74.53 % 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: 0.71 (0.30), residues: 790 helix: 1.46 (0.26), residues: 400 sheet: 1.03 (0.77), residues: 48 loop : -0.80 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 566 HIS 0.005 0.001 HIS A 265 PHE 0.031 0.002 PHE A 369 TYR 0.021 0.002 TYR B 380 ARG 0.004 0.000 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 207 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 SER cc_start: 0.7349 (m) cc_final: 0.7044 (t) REVERT: A 50 TYR cc_start: 0.6259 (t80) cc_final: 0.6044 (t80) REVERT: A 61 ASN cc_start: 0.5964 (m-40) cc_final: 0.5658 (m110) REVERT: A 62 MET cc_start: 0.7466 (ttt) cc_final: 0.7005 (ttp) REVERT: A 63 ASN cc_start: 0.6998 (m-40) cc_final: 0.6298 (m-40) REVERT: A 64 ASN cc_start: 0.7668 (m-40) cc_final: 0.7364 (m110) REVERT: A 67 ASP cc_start: 0.7092 (m-30) cc_final: 0.6779 (m-30) REVERT: A 74 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7793 (ttpt) REVERT: A 98 GLN cc_start: 0.7574 (tp40) cc_final: 0.7023 (mp10) REVERT: A 129 THR cc_start: 0.7489 (t) cc_final: 0.7228 (p) REVERT: A 131 LYS cc_start: 0.6600 (pttm) cc_final: 0.6325 (ptmm) REVERT: A 150 GLU cc_start: 0.6869 (tm-30) cc_final: 0.6614 (tm-30) REVERT: A 160 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6375 (tm-30) REVERT: A 192 ARG cc_start: 0.7384 (mtt-85) cc_final: 0.7006 (mpp-170) REVERT: A 201 ASP cc_start: 0.7280 (t70) cc_final: 0.6929 (m-30) REVERT: A 202 TYR cc_start: 0.7773 (t80) cc_final: 0.7492 (t80) REVERT: A 206 ASP cc_start: 0.7698 (t0) cc_final: 0.7302 (t0) REVERT: A 219 ARG cc_start: 0.7641 (mtt90) cc_final: 0.7381 (mtt90) REVERT: A 270 MET cc_start: 0.7376 (tpp) cc_final: 0.7163 (tpt) REVERT: A 285 PHE cc_start: 0.6737 (m-80) cc_final: 0.6340 (m-10) REVERT: A 291 ILE cc_start: 0.7546 (mt) cc_final: 0.7229 (mp) REVERT: A 302 TRP cc_start: 0.6463 (m-10) cc_final: 0.6170 (m-10) REVERT: A 310 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6415 (mp0) REVERT: A 360 MET cc_start: 0.7563 (ttp) cc_final: 0.7317 (ptm) REVERT: A 408 MET cc_start: 0.7235 (tpp) cc_final: 0.6814 (mtp) REVERT: A 455 MET cc_start: 0.7412 (tpt) cc_final: 0.6898 (tpt) REVERT: A 467 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6649 (mt-10) REVERT: A 470 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7291 (tppp) REVERT: A 472 GLN cc_start: 0.8010 (mt0) cc_final: 0.7399 (mp10) REVERT: A 475 LYS cc_start: 0.7379 (ttpt) cc_final: 0.7063 (ptmm) REVERT: A 480 MET cc_start: 0.6123 (ttm) cc_final: 0.5692 (ttm) REVERT: A 482 ARG cc_start: 0.7022 (ttm170) cc_final: 0.6810 (mtt180) REVERT: A 483 GLU cc_start: 0.6668 (tp30) cc_final: 0.6330 (tp30) REVERT: A 488 VAL cc_start: 0.7672 (p) cc_final: 0.7127 (t) REVERT: A 518 ARG cc_start: 0.6952 (ttp80) cc_final: 0.6258 (ttp80) REVERT: A 536 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6925 (tp30) REVERT: A 539 LEU cc_start: 0.7964 (tp) cc_final: 0.7723 (tt) REVERT: A 541 LYS cc_start: 0.7272 (ptpp) cc_final: 0.6477 (ptpp) REVERT: A 564 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7063 (mm-30) REVERT: A 582 ARG cc_start: 0.6549 (mmm160) cc_final: 0.6215 (mmm160) REVERT: A 610 TRP cc_start: 0.7240 (t60) cc_final: 0.6872 (t60) REVERT: A 613 TYR cc_start: 0.6156 (p90) cc_final: 0.5601 (p90) REVERT: B 396 TYR cc_start: 0.7068 (m-80) cc_final: 0.6334 (m-80) REVERT: B 409 GLN cc_start: 0.7997 (mt0) cc_final: 0.7619 (mt0) REVERT: B 422 ASN cc_start: 0.7255 (m-40) cc_final: 0.6742 (m-40) REVERT: B 430 THR cc_start: 0.7903 (OUTLIER) cc_final: 0.7661 (t) REVERT: B 453 TYR cc_start: 0.7946 (p90) cc_final: 0.7442 (p90) REVERT: B 454 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7636 (ttm-80) REVERT: B 457 ARG cc_start: 0.6517 (ttt90) cc_final: 0.6088 (ttp-170) REVERT: B 509 ARG cc_start: 0.7716 (mtt180) cc_final: 0.7125 (mtt180) outliers start: 25 outliers final: 8 residues processed: 217 average time/residue: 1.0636 time to fit residues: 243.4694 Evaluate side-chains 215 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 203 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.2980 chunk 42 optimal weight: 0.2980 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 0.0870 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.0670 chunk 30 optimal weight: 0.1980 chunk 44 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 overall best weight: 0.1696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 345 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN B 448 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6690 Z= 0.200 Angle : 0.611 8.739 9097 Z= 0.315 Chirality : 0.048 0.432 968 Planarity : 0.005 0.042 1172 Dihedral : 5.081 41.513 987 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.17 % Allowed : 22.30 % Favored : 74.53 % 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: 0.76 (0.30), residues: 790 helix: 1.51 (0.26), residues: 397 sheet: 1.02 (0.80), residues: 48 loop : -0.76 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 566 HIS 0.005 0.001 HIS A 417 PHE 0.034 0.002 PHE A 369 TYR 0.017 0.002 TYR B 380 ARG 0.005 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 212 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7029 (mttm) cc_final: 0.6761 (mttm) REVERT: A 47 SER cc_start: 0.7321 (m) cc_final: 0.7039 (t) REVERT: A 61 ASN cc_start: 0.5968 (m-40) cc_final: 0.5665 (m110) REVERT: A 62 MET cc_start: 0.7477 (ttt) cc_final: 0.7021 (ttp) REVERT: A 63 ASN cc_start: 0.7005 (m-40) cc_final: 0.6293 (m-40) REVERT: A 64 ASN cc_start: 0.7704 (m-40) cc_final: 0.7398 (m110) REVERT: A 67 ASP cc_start: 0.7067 (m-30) cc_final: 0.6738 (m-30) REVERT: A 74 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7783 (ttpt) REVERT: A 98 GLN cc_start: 0.7613 (tp40) cc_final: 0.7155 (mm-40) REVERT: A 129 THR cc_start: 0.7506 (t) cc_final: 0.7182 (p) REVERT: A 131 LYS cc_start: 0.6589 (pttm) cc_final: 0.6333 (ptmm) REVERT: A 154 ASN cc_start: 0.6613 (m110) cc_final: 0.6403 (m-40) REVERT: A 192 ARG cc_start: 0.7410 (mtt-85) cc_final: 0.6876 (mpp80) REVERT: A 201 ASP cc_start: 0.7270 (t70) cc_final: 0.6977 (m-30) REVERT: A 202 TYR cc_start: 0.7770 (t80) cc_final: 0.7478 (t80) REVERT: A 206 ASP cc_start: 0.7711 (t0) cc_final: 0.7062 (t0) REVERT: A 270 MET cc_start: 0.7328 (tpp) cc_final: 0.7049 (tpt) REVERT: A 307 ILE cc_start: 0.7715 (mt) cc_final: 0.7501 (mt) REVERT: A 357 ARG cc_start: 0.7117 (mtt180) cc_final: 0.6880 (mtt-85) REVERT: A 408 MET cc_start: 0.7260 (tpp) cc_final: 0.6855 (mtp) REVERT: A 455 MET cc_start: 0.7408 (tpt) cc_final: 0.6860 (tpt) REVERT: A 470 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7389 (tptp) REVERT: A 475 LYS cc_start: 0.7384 (ttpt) cc_final: 0.7156 (ptmm) REVERT: A 480 MET cc_start: 0.6187 (ttm) cc_final: 0.5729 (ttm) REVERT: A 482 ARG cc_start: 0.7045 (ttm170) cc_final: 0.6620 (mtt180) REVERT: A 483 GLU cc_start: 0.6674 (tp30) cc_final: 0.6324 (tp30) REVERT: A 488 VAL cc_start: 0.7692 (p) cc_final: 0.7013 (t) REVERT: A 509 ASP cc_start: 0.6858 (t0) cc_final: 0.6580 (t70) REVERT: A 518 ARG cc_start: 0.6961 (ttp80) cc_final: 0.6434 (ttp80) REVERT: A 539 LEU cc_start: 0.8023 (tp) cc_final: 0.7778 (tt) REVERT: A 541 LYS cc_start: 0.7271 (ptpp) cc_final: 0.6472 (ptpp) REVERT: A 564 GLU cc_start: 0.7282 (mm-30) cc_final: 0.7048 (mm-30) REVERT: A 582 ARG cc_start: 0.6524 (mmm160) cc_final: 0.6165 (mmm160) REVERT: A 594 TRP cc_start: 0.5932 (t60) cc_final: 0.5409 (t60) REVERT: A 610 TRP cc_start: 0.7215 (t60) cc_final: 0.6926 (t60) REVERT: A 613 TYR cc_start: 0.6158 (p90) cc_final: 0.5505 (p90) REVERT: B 396 TYR cc_start: 0.7105 (m-80) cc_final: 0.6330 (m-80) REVERT: B 409 GLN cc_start: 0.8006 (mt0) cc_final: 0.7583 (mt0) REVERT: B 422 ASN cc_start: 0.7266 (m-40) cc_final: 0.6763 (m-40) REVERT: B 430 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7594 (t) REVERT: B 453 TYR cc_start: 0.7914 (p90) cc_final: 0.7440 (p90) REVERT: B 454 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7474 (ttm-80) REVERT: B 457 ARG cc_start: 0.6561 (ttt90) cc_final: 0.6108 (ttp-170) REVERT: B 509 ARG cc_start: 0.7686 (mtt180) cc_final: 0.7179 (mtt180) outliers start: 22 outliers final: 11 residues processed: 222 average time/residue: 1.0637 time to fit residues: 248.7116 Evaluate side-chains 224 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 210 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.0970 chunk 47 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 59 optimal weight: 0.0070 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 81 GLN A 345 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 487 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 6690 Z= 0.261 Angle : 0.663 9.380 9097 Z= 0.342 Chirality : 0.050 0.359 968 Planarity : 0.005 0.043 1172 Dihedral : 5.188 40.356 987 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.60 % Allowed : 23.17 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.66 (0.30), residues: 790 helix: 1.47 (0.26), residues: 397 sheet: 1.13 (0.81), residues: 48 loop : -0.90 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 302 HIS 0.006 0.001 HIS A 378 PHE 0.031 0.002 PHE A 369 TYR 0.025 0.002 TYR B 380 ARG 0.005 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 210 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.6986 (mttm) cc_final: 0.6712 (mttm) REVERT: A 61 ASN cc_start: 0.5922 (m-40) cc_final: 0.5667 (m-40) REVERT: A 62 MET cc_start: 0.7438 (ttt) cc_final: 0.7190 (ttp) REVERT: A 63 ASN cc_start: 0.7040 (m-40) cc_final: 0.6321 (m-40) REVERT: A 64 ASN cc_start: 0.7707 (m-40) cc_final: 0.7401 (m110) REVERT: A 67 ASP cc_start: 0.7092 (m-30) cc_final: 0.6785 (m-30) REVERT: A 74 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7787 (ttpt) REVERT: A 98 GLN cc_start: 0.7628 (tp40) cc_final: 0.7146 (mm-40) REVERT: A 129 THR cc_start: 0.7507 (t) cc_final: 0.7207 (p) REVERT: A 131 LYS cc_start: 0.6565 (pttm) cc_final: 0.6204 (ttmm) REVERT: A 192 ARG cc_start: 0.7433 (mtt-85) cc_final: 0.6892 (mpp80) REVERT: A 201 ASP cc_start: 0.7227 (t70) cc_final: 0.6997 (m-30) REVERT: A 202 TYR cc_start: 0.7772 (t80) cc_final: 0.7506 (t80) REVERT: A 206 ASP cc_start: 0.7674 (t0) cc_final: 0.7184 (t0) REVERT: A 270 MET cc_start: 0.7407 (tpp) cc_final: 0.7154 (tpt) REVERT: A 455 MET cc_start: 0.7376 (tpt) cc_final: 0.6738 (tpt) REVERT: A 470 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7355 (tppp) REVERT: A 475 LYS cc_start: 0.7395 (ttpt) cc_final: 0.7177 (ptmm) REVERT: A 480 MET cc_start: 0.6166 (ttm) cc_final: 0.5668 (ttm) REVERT: A 483 GLU cc_start: 0.6680 (tp30) cc_final: 0.6348 (tp30) REVERT: A 488 VAL cc_start: 0.7688 (p) cc_final: 0.7299 (t) REVERT: A 489 GLU cc_start: 0.5942 (pm20) cc_final: 0.5505 (pm20) REVERT: A 509 ASP cc_start: 0.6955 (t0) cc_final: 0.6657 (t70) REVERT: A 518 ARG cc_start: 0.6973 (ttp80) cc_final: 0.6478 (ttp80) REVERT: A 539 LEU cc_start: 0.8041 (tp) cc_final: 0.7790 (tt) REVERT: A 564 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7077 (mm-30) REVERT: A 610 TRP cc_start: 0.7240 (t60) cc_final: 0.6878 (t60) REVERT: B 409 GLN cc_start: 0.8008 (mt0) cc_final: 0.7763 (mt0) REVERT: B 422 ASN cc_start: 0.7276 (m-40) cc_final: 0.6790 (m-40) REVERT: B 430 THR cc_start: 0.7947 (OUTLIER) cc_final: 0.7680 (t) REVERT: B 453 TYR cc_start: 0.7935 (p90) cc_final: 0.7447 (p90) REVERT: B 454 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7473 (ttm-80) REVERT: B 457 ARG cc_start: 0.6514 (ttt90) cc_final: 0.6115 (ttp-170) REVERT: B 509 ARG cc_start: 0.7713 (mtt180) cc_final: 0.7148 (mtt180) outliers start: 25 outliers final: 15 residues processed: 221 average time/residue: 1.0559 time to fit residues: 245.8617 Evaluate side-chains 221 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 203 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 380 GLN Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 0.0570 chunk 45 optimal weight: 0.4980 chunk 35 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 345 HIS A 397 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 ASN B 417 ASN B 448 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 6690 Z= 0.272 Angle : 0.688 9.154 9097 Z= 0.352 Chirality : 0.050 0.359 968 Planarity : 0.005 0.060 1172 Dihedral : 5.122 39.492 987 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.45 % Allowed : 24.17 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.30), residues: 790 helix: 1.39 (0.26), residues: 396 sheet: 1.70 (0.81), residues: 43 loop : -0.99 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 302 HIS 0.006 0.001 HIS A 378 PHE 0.033 0.002 PHE A 369 TYR 0.024 0.002 TYR B 380 ARG 0.013 0.001 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 205 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.5574 (mp) cc_final: 0.5305 (mp) REVERT: A 26 LYS cc_start: 0.7074 (mttm) cc_final: 0.6795 (mttm) REVERT: A 47 SER cc_start: 0.7419 (m) cc_final: 0.7121 (t) REVERT: A 61 ASN cc_start: 0.5849 (m-40) cc_final: 0.5566 (m-40) REVERT: A 62 MET cc_start: 0.7455 (ttt) cc_final: 0.7177 (ttp) REVERT: A 63 ASN cc_start: 0.7001 (m-40) cc_final: 0.6290 (m-40) REVERT: A 64 ASN cc_start: 0.7715 (m-40) cc_final: 0.7403 (m110) REVERT: A 67 ASP cc_start: 0.7092 (m-30) cc_final: 0.6766 (m-30) REVERT: A 74 LYS cc_start: 0.8160 (ttpt) cc_final: 0.7758 (ttpt) REVERT: A 98 GLN cc_start: 0.7627 (tp40) cc_final: 0.7124 (mm-40) REVERT: A 129 THR cc_start: 0.7567 (t) cc_final: 0.7241 (p) REVERT: A 131 LYS cc_start: 0.6554 (pttm) cc_final: 0.6215 (ttmm) REVERT: A 160 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6558 (tt0) REVERT: A 192 ARG cc_start: 0.7411 (mtt-85) cc_final: 0.6977 (mpp80) REVERT: A 201 ASP cc_start: 0.7237 (t70) cc_final: 0.7021 (m-30) REVERT: A 202 TYR cc_start: 0.7765 (t80) cc_final: 0.7266 (t80) REVERT: A 206 ASP cc_start: 0.7634 (t0) cc_final: 0.7132 (t0) REVERT: A 291 ILE cc_start: 0.7509 (mt) cc_final: 0.7198 (mp) REVERT: A 357 ARG cc_start: 0.7127 (mtt180) cc_final: 0.6883 (mtt-85) REVERT: A 408 MET cc_start: 0.7149 (tpp) cc_final: 0.6832 (ttp) REVERT: A 455 MET cc_start: 0.7394 (tpt) cc_final: 0.6719 (tpt) REVERT: A 470 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7398 (tppp) REVERT: A 475 LYS cc_start: 0.7361 (ttpt) cc_final: 0.7146 (ptmm) REVERT: A 480 MET cc_start: 0.6253 (ttm) cc_final: 0.5752 (ttm) REVERT: A 482 ARG cc_start: 0.7074 (ttm170) cc_final: 0.6614 (mtt180) REVERT: A 483 GLU cc_start: 0.6672 (tp30) cc_final: 0.6335 (tp30) REVERT: A 488 VAL cc_start: 0.7719 (p) cc_final: 0.6954 (t) REVERT: A 489 GLU cc_start: 0.5945 (pm20) cc_final: 0.5102 (pm20) REVERT: A 509 ASP cc_start: 0.6967 (t0) cc_final: 0.6672 (t70) REVERT: A 518 ARG cc_start: 0.6974 (ttp80) cc_final: 0.6476 (ttp80) REVERT: A 536 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6781 (mt-10) REVERT: A 539 LEU cc_start: 0.8048 (tp) cc_final: 0.7802 (tt) REVERT: A 541 LYS cc_start: 0.7343 (ptpp) cc_final: 0.6616 (ptpp) REVERT: A 564 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7101 (mm-30) REVERT: A 610 TRP cc_start: 0.7253 (t60) cc_final: 0.6941 (t60) REVERT: B 409 GLN cc_start: 0.7976 (mt0) cc_final: 0.7736 (mt0) REVERT: B 422 ASN cc_start: 0.7275 (m-40) cc_final: 0.6822 (m-40) REVERT: B 430 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7710 (t) REVERT: B 453 TYR cc_start: 0.7981 (p90) cc_final: 0.7480 (p90) REVERT: B 454 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7511 (ttm-80) REVERT: B 457 ARG cc_start: 0.6572 (ttt90) cc_final: 0.6147 (ttp-170) REVERT: B 509 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7336 (mtt180) outliers start: 24 outliers final: 13 residues processed: 218 average time/residue: 1.0641 time to fit residues: 244.1659 Evaluate side-chains 223 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 206 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 380 GLN Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.5980 chunk 71 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 6 optimal weight: 0.0970 chunk 47 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 57 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 overall best weight: 0.2378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 397 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6690 Z= 0.253 Angle : 0.693 9.122 9097 Z= 0.354 Chirality : 0.049 0.353 968 Planarity : 0.005 0.075 1172 Dihedral : 5.110 39.530 987 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.02 % Allowed : 24.32 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.52 (0.30), residues: 790 helix: 1.35 (0.26), residues: 396 sheet: 1.59 (0.78), residues: 43 loop : -1.00 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 302 HIS 0.005 0.001 HIS A 378 PHE 0.034 0.002 PHE A 369 TYR 0.025 0.002 TYR A 158 ARG 0.018 0.001 ARG A 582 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 208 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7008 (mttm) cc_final: 0.6731 (mttm) REVERT: A 47 SER cc_start: 0.7407 (m) cc_final: 0.7111 (t) REVERT: A 57 GLU cc_start: 0.7506 (pm20) cc_final: 0.7220 (pm20) REVERT: A 61 ASN cc_start: 0.5869 (m-40) cc_final: 0.5586 (m-40) REVERT: A 62 MET cc_start: 0.7423 (ttt) cc_final: 0.7205 (ttp) REVERT: A 63 ASN cc_start: 0.7038 (m-40) cc_final: 0.6322 (m-40) REVERT: A 64 ASN cc_start: 0.7711 (m-40) cc_final: 0.7405 (m110) REVERT: A 67 ASP cc_start: 0.7087 (m-30) cc_final: 0.6780 (m-30) REVERT: A 74 LYS cc_start: 0.8153 (ttpt) cc_final: 0.7754 (ttpt) REVERT: A 86 GLN cc_start: 0.7100 (pm20) cc_final: 0.6860 (pm20) REVERT: A 98 GLN cc_start: 0.7630 (tp40) cc_final: 0.7132 (mm-40) REVERT: A 129 THR cc_start: 0.7559 (t) cc_final: 0.7229 (p) REVERT: A 131 LYS cc_start: 0.6556 (pttm) cc_final: 0.6222 (ttmm) REVERT: A 160 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6378 (tm-30) REVERT: A 192 ARG cc_start: 0.7413 (mtt-85) cc_final: 0.6976 (mpp80) REVERT: A 201 ASP cc_start: 0.7272 (t70) cc_final: 0.7017 (m-30) REVERT: A 202 TYR cc_start: 0.7785 (t80) cc_final: 0.7340 (t80) REVERT: A 206 ASP cc_start: 0.7637 (t0) cc_final: 0.7111 (t0) REVERT: A 238 GLU cc_start: 0.6412 (tp30) cc_final: 0.6182 (tp30) REVERT: A 309 LYS cc_start: 0.7754 (tppp) cc_final: 0.7553 (mmmm) REVERT: A 330 ASN cc_start: 0.7424 (p0) cc_final: 0.7019 (p0) REVERT: A 357 ARG cc_start: 0.7147 (mtt180) cc_final: 0.6880 (mtt-85) REVERT: A 358 ILE cc_start: 0.7680 (mt) cc_final: 0.7409 (mt) REVERT: A 408 MET cc_start: 0.7120 (tpp) cc_final: 0.6789 (ttp) REVERT: A 455 MET cc_start: 0.7380 (tpt) cc_final: 0.6708 (tpt) REVERT: A 470 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7430 (tppp) REVERT: A 475 LYS cc_start: 0.7362 (ttpt) cc_final: 0.7149 (ptmm) REVERT: A 480 MET cc_start: 0.6260 (ttm) cc_final: 0.5763 (ttm) REVERT: A 482 ARG cc_start: 0.7071 (ttm170) cc_final: 0.6624 (mtt180) REVERT: A 483 GLU cc_start: 0.6672 (tp30) cc_final: 0.6336 (tp30) REVERT: A 488 VAL cc_start: 0.7710 (p) cc_final: 0.6940 (t) REVERT: A 489 GLU cc_start: 0.5934 (pm20) cc_final: 0.5150 (pm20) REVERT: A 509 ASP cc_start: 0.6951 (t70) cc_final: 0.6673 (t70) REVERT: A 518 ARG cc_start: 0.6953 (ttp80) cc_final: 0.6457 (ttp80) REVERT: A 536 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6876 (mm-30) REVERT: A 539 LEU cc_start: 0.8046 (tp) cc_final: 0.7801 (tt) REVERT: A 541 LYS cc_start: 0.7359 (ptpp) cc_final: 0.6531 (ptpp) REVERT: A 564 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7095 (mm-30) REVERT: A 582 ARG cc_start: 0.6572 (mmm160) cc_final: 0.6350 (mmm160) REVERT: A 610 TRP cc_start: 0.7251 (t60) cc_final: 0.6864 (t60) REVERT: B 409 GLN cc_start: 0.7970 (mt0) cc_final: 0.7682 (mt0) REVERT: B 422 ASN cc_start: 0.7303 (m-40) cc_final: 0.6861 (m-40) REVERT: B 430 THR cc_start: 0.7969 (OUTLIER) cc_final: 0.7704 (t) REVERT: B 453 TYR cc_start: 0.7976 (p90) cc_final: 0.7418 (p90) REVERT: B 454 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7499 (ttm-80) REVERT: B 457 ARG cc_start: 0.6500 (ttt90) cc_final: 0.6105 (ttp-170) REVERT: B 509 ARG cc_start: 0.7729 (mtt180) cc_final: 0.7337 (mtt180) outliers start: 21 outliers final: 12 residues processed: 218 average time/residue: 1.0536 time to fit residues: 242.1012 Evaluate side-chains 222 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 454 ARG Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 494 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.3980 chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 63 optimal weight: 0.1980 chunk 7 optimal weight: 0.0570 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 chunk 70 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 overall best weight: 0.1498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 397 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 ASN B 417 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.178316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.163132 restraints weight = 21911.290| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 4.31 r_work: 0.4056 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4058 r_free = 0.4058 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4058 r_free = 0.4058 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6690 Z= 0.224 Angle : 0.679 9.032 9097 Z= 0.347 Chirality : 0.048 0.351 968 Planarity : 0.005 0.075 1172 Dihedral : 5.044 39.592 987 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.59 % Allowed : 25.32 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.60 (0.30), residues: 790 helix: 1.40 (0.26), residues: 396 sheet: 1.47 (0.76), residues: 45 loop : -0.92 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 302 HIS 0.005 0.001 HIS A 540 PHE 0.031 0.002 PHE A 369 TYR 0.024 0.002 TYR B 380 ARG 0.018 0.001 ARG A 582 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4534.27 seconds wall clock time: 79 minutes 23.68 seconds (4763.68 seconds total)