Starting phenix.real_space_refine on Sat Aug 3 01:49:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whz_37553/08_2024/8whz_37553.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whz_37553/08_2024/8whz_37553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whz_37553/08_2024/8whz_37553.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whz_37553/08_2024/8whz_37553.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whz_37553/08_2024/8whz_37553.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whz_37553/08_2024/8whz_37553.cif" } resolution = 3.93 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= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 Cl 1 4.86 5 C 4173 2.51 5 N 1073 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 GLU 57": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B GLU 471": "OE1" <-> "OE2" 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: 6515 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "B" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 13, 'TRANS': 180} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.78, per 1000 atoms: 0.73 Number of scatterers: 6515 At special positions: 0 Unit cell: (75.97, 95.23, 114.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 37 16.00 O 1230 8.00 N 1073 7.00 C 4173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 903 " - " ASN A 546 " " NAG A 904 " - " ASN A 90 " " NAG A 905 " - " ASN A 322 " " NAG A 906 " - " ASN A 53 " " NAG B 601 " - " ASN B 354 " " NAG B 602 " - " ASN B 343 " Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 57.1% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 3.795A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.802A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.312A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.425A 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 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.752A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.918A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.743A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.685A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.642A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.240A 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 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.753A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.827A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.532A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix 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 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.894A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.806A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.788A 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: 3.666A pdb=" N THR A 347 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 359 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 6.153A 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: 3.875A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.523A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) 315 hydrogen bonds defined for protein. 903 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: 1.72 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1864 1.33 - 1.46: 1357 1.46 - 1.58: 3422 1.58 - 1.70: 1 1.70 - 1.82: 58 Bond restraints: 6702 Sorted by residual: bond pdb=" C THR A 27 " pdb=" N PHE A 28 " ideal model delta sigma weight residual 1.335 1.292 0.043 1.30e-02 5.92e+03 1.12e+01 bond pdb=" N THR A 27 " pdb=" CA THR A 27 " ideal model delta sigma weight residual 1.459 1.421 0.038 1.17e-02 7.31e+03 1.08e+01 bond pdb=" CA ARG B 457 " pdb=" CB ARG B 457 " ideal model delta sigma weight residual 1.534 1.480 0.053 1.78e-02 3.16e+03 8.94e+00 bond pdb=" CA THR A 27 " pdb=" C THR A 27 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.24e-02 6.50e+03 6.85e+00 bond pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.30e+00 ... (remaining 6697 not shown) Histogram of bond angle deviations from ideal: 97.52 - 104.83: 128 104.83 - 112.15: 3132 112.15 - 119.46: 2348 119.46 - 126.77: 3367 126.77 - 134.09: 135 Bond angle restraints: 9110 Sorted by residual: angle pdb=" N LYS A 313 " pdb=" CA LYS A 313 " pdb=" C LYS A 313 " ideal model delta sigma weight residual 111.82 106.74 5.08 1.16e+00 7.43e-01 1.92e+01 angle pdb=" CA PRO B 384 " pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 112.00 106.33 5.67 1.40e+00 5.10e-01 1.64e+01 angle pdb=" N CYS A 498 " pdb=" CA CYS A 498 " pdb=" C CYS A 498 " ideal model delta sigma weight residual 110.44 105.84 4.60 1.20e+00 6.94e-01 1.47e+01 angle pdb=" CA ARG B 457 " pdb=" C ARG B 457 " pdb=" N LYS B 458 " ideal model delta sigma weight residual 115.61 120.89 -5.28 1.45e+00 4.76e-01 1.32e+01 angle pdb=" N VAL A 364 " pdb=" CA VAL A 364 " pdb=" C VAL A 364 " ideal model delta sigma weight residual 106.21 109.67 -3.46 1.07e+00 8.73e-01 1.05e+01 ... (remaining 9105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3628 17.95 - 35.90: 318 35.90 - 53.85: 58 53.85 - 71.80: 17 71.80 - 89.75: 8 Dihedral angle restraints: 4029 sinusoidal: 1705 harmonic: 2324 Sorted by residual: dihedral pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta harmonic sigma weight residual 180.00 143.36 36.64 0 5.00e+00 4.00e-02 5.37e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 134.85 -41.85 1 1.00e+01 1.00e-02 2.45e+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 93.00 129.35 -36.35 1 1.00e+01 1.00e-02 1.87e+01 ... (remaining 4026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 705 0.049 - 0.097: 202 0.097 - 0.146: 54 0.146 - 0.194: 2 0.194 - 0.243: 1 Chirality restraints: 964 Sorted by residual: chirality pdb=" C1 NAG A 905 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 905 " pdb=" O5 NAG A 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA PRO B 384 " pdb=" N PRO B 384 " pdb=" C PRO B 384 " pdb=" CB PRO B 384 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" CG LEU B 492 " pdb=" CB LEU B 492 " pdb=" CD1 LEU B 492 " pdb=" CD2 LEU B 492 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 961 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 383 " -0.072 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO B 384 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 69 " -0.016 2.00e-02 2.50e+03 1.13e-02 3.22e+00 pdb=" CG TRP A 69 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 69 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 69 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 69 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 69 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 69 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 69 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 69 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 69 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 506 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO B 507 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 507 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 507 " 0.021 5.00e-02 4.00e+02 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 45 2.48 - 3.08: 4740 3.08 - 3.69: 10301 3.69 - 4.29: 14541 4.29 - 4.90: 22781 Nonbonded interactions: 52408 Sorted by model distance: nonbonded pdb=" O TYR B 421 " pdb=" CZ ARG B 457 " model vdw 1.873 3.270 nonbonded pdb=" O TYR B 421 " pdb=" NH1 ARG B 457 " model vdw 1.994 3.120 nonbonded pdb=" NH2 ARG B 454 " pdb=" CG ARG B 457 " model vdw 2.068 3.520 nonbonded pdb=" O LEU A 156 " pdb=" OH TYR A 252 " model vdw 2.142 3.040 nonbonded pdb=" CZ ARG B 454 " pdb=" NE ARG B 457 " model vdw 2.171 3.350 ... (remaining 52403 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 26.470 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 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 : 0.004 0.091 6702 Z= 0.254 Angle : 0.791 9.421 9110 Z= 0.456 Chirality : 0.047 0.243 964 Planarity : 0.006 0.105 1172 Dihedral : 14.476 89.752 2516 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 0.29 % Allowed : 0.29 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.54 (0.30), residues: 787 helix: 0.61 (0.26), residues: 390 sheet: -0.55 (0.89), residues: 35 loop : -1.43 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 69 HIS 0.004 0.001 HIS A 493 PHE 0.014 0.002 PHE A 230 TYR 0.020 0.002 TYR A 454 ARG 0.006 0.001 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.6456 (mtp) cc_final: 0.6177 (mmm) REVERT: A 243 TYR cc_start: 0.9040 (t80) cc_final: 0.8669 (t80) REVERT: A 270 MET cc_start: 0.7170 (tpt) cc_final: 0.6916 (tpt) REVERT: A 333 LEU cc_start: 0.9346 (mt) cc_final: 0.9130 (mm) REVERT: A 408 MET cc_start: 0.8318 (mmp) cc_final: 0.8081 (mmt) REVERT: A 461 TRP cc_start: 0.8963 (m-10) cc_final: 0.8732 (m-10) REVERT: A 484 ILE cc_start: 0.8728 (mm) cc_final: 0.8257 (tp) REVERT: B 406 GLU cc_start: 0.8224 (mp0) cc_final: 0.8015 (mp0) outliers start: 2 outliers final: 1 residues processed: 202 average time/residue: 0.2122 time to fit residues: 54.6382 Evaluate side-chains 124 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 GLN ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN B 417 ASN B 505 HIS ** 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: 0.7490 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6702 Z= 0.252 Angle : 0.688 7.665 9110 Z= 0.360 Chirality : 0.046 0.217 964 Planarity : 0.005 0.054 1172 Dihedral : 6.010 51.658 985 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 2.45 % Allowed : 11.08 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.33 (0.29), residues: 787 helix: 0.64 (0.25), residues: 406 sheet: -0.33 (0.80), residues: 42 loop : -1.22 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 165 HIS 0.005 0.001 HIS A 417 PHE 0.033 0.002 PHE B 375 TYR 0.021 0.002 TYR B 421 ARG 0.009 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7033 (mtp) cc_final: 0.6737 (mmm) REVERT: A 176 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7018 (mm) REVERT: A 190 MET cc_start: 0.7766 (ptp) cc_final: 0.7519 (ptp) REVERT: A 243 TYR cc_start: 0.9010 (t80) cc_final: 0.8686 (t80) REVERT: A 250 ASN cc_start: 0.8692 (t0) cc_final: 0.8351 (m110) REVERT: A 323 MET cc_start: 0.8264 (mmt) cc_final: 0.7144 (mmm) REVERT: A 360 MET cc_start: 0.8146 (ppp) cc_final: 0.7486 (ppp) REVERT: A 366 MET cc_start: 0.8669 (ppp) cc_final: 0.7860 (ppp) REVERT: A 594 TRP cc_start: 0.8150 (t-100) cc_final: 0.7899 (t-100) REVERT: B 347 PHE cc_start: 0.6432 (m-80) cc_final: 0.5985 (m-80) outliers start: 17 outliers final: 7 residues processed: 137 average time/residue: 0.1788 time to fit residues: 32.6385 Evaluate side-chains 115 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 453 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN A 508 ASN B 417 ASN B 505 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6702 Z= 0.228 Angle : 0.639 6.660 9110 Z= 0.339 Chirality : 0.045 0.205 964 Planarity : 0.005 0.050 1172 Dihedral : 5.788 46.767 984 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.06 % Rotamer: Outliers : 2.88 % Allowed : 14.82 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.30 (0.29), residues: 787 helix: 0.62 (0.25), residues: 406 sheet: 0.19 (0.81), residues: 42 loop : -1.24 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 594 HIS 0.004 0.001 HIS A 34 PHE 0.019 0.002 PHE A 369 TYR 0.016 0.002 TYR A 237 ARG 0.003 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7339 (mtp) cc_final: 0.7015 (mmm) REVERT: A 243 TYR cc_start: 0.8980 (t80) cc_final: 0.8634 (t80) REVERT: A 323 MET cc_start: 0.8496 (mmt) cc_final: 0.7172 (mmm) REVERT: A 333 LEU cc_start: 0.9188 (mt) cc_final: 0.8864 (mm) REVERT: A 366 MET cc_start: 0.8727 (ppp) cc_final: 0.7910 (ppp) REVERT: A 376 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7664 (tpt) REVERT: B 369 TYR cc_start: 0.7191 (m-80) cc_final: 0.6971 (m-80) REVERT: B 406 GLU cc_start: 0.8241 (mp0) cc_final: 0.7930 (mp0) REVERT: B 417 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8499 (t0) outliers start: 20 outliers final: 11 residues processed: 134 average time/residue: 0.1899 time to fit residues: 33.9264 Evaluate side-chains 115 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 453 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS A 378 HIS A 472 GLN A 508 ASN A 598 GLN B 493 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6702 Z= 0.196 Angle : 0.603 6.655 9110 Z= 0.322 Chirality : 0.044 0.206 964 Planarity : 0.004 0.044 1172 Dihedral : 5.463 37.923 984 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer: Outliers : 2.45 % Allowed : 16.98 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.06 (0.29), residues: 787 helix: 0.84 (0.25), residues: 400 sheet: 0.48 (0.79), residues: 42 loop : -1.15 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 594 HIS 0.004 0.001 HIS A 374 PHE 0.032 0.002 PHE B 375 TYR 0.013 0.002 TYR A 237 ARG 0.004 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.8340 (mtm) cc_final: 0.8035 (mtp) REVERT: A 270 MET cc_start: 0.7337 (tpt) cc_final: 0.6809 (tpt) REVERT: A 366 MET cc_start: 0.8689 (ppp) cc_final: 0.7882 (ppp) REVERT: A 406 GLU cc_start: 0.8489 (tp30) cc_final: 0.8233 (mm-30) REVERT: A 441 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8349 (ttpp) REVERT: B 406 GLU cc_start: 0.8214 (mp0) cc_final: 0.7974 (mp0) outliers start: 17 outliers final: 12 residues processed: 126 average time/residue: 0.1763 time to fit residues: 30.1506 Evaluate side-chains 109 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 52 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN A 472 GLN B 417 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6702 Z= 0.224 Angle : 0.608 8.232 9110 Z= 0.321 Chirality : 0.044 0.200 964 Planarity : 0.005 0.053 1172 Dihedral : 5.333 38.588 984 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.93 % Rotamer: Outliers : 4.17 % Allowed : 17.27 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.11 (0.29), residues: 787 helix: 0.79 (0.25), residues: 406 sheet: 0.42 (0.78), residues: 42 loop : -1.18 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 473 HIS 0.005 0.001 HIS A 374 PHE 0.015 0.002 PHE A 369 TYR 0.015 0.002 TYR B 351 ARG 0.003 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7561 (mmm) cc_final: 0.7305 (mmm) REVERT: A 163 TRP cc_start: 0.8595 (t-100) cc_final: 0.8012 (t60) REVERT: A 249 MET cc_start: 0.8341 (mtm) cc_final: 0.8039 (mtp) REVERT: A 323 MET cc_start: 0.8542 (mmm) cc_final: 0.6966 (mmm) REVERT: A 360 MET cc_start: 0.7940 (ppp) cc_final: 0.7716 (ppp) REVERT: A 361 CYS cc_start: 0.5320 (OUTLIER) cc_final: 0.4801 (p) REVERT: A 366 MET cc_start: 0.8714 (ppp) cc_final: 0.7891 (ppp) REVERT: A 376 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7581 (tpt) REVERT: A 406 GLU cc_start: 0.8589 (tp30) cc_final: 0.8357 (mm-30) REVERT: A 441 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8387 (ttpp) REVERT: B 406 GLU cc_start: 0.8366 (mp0) cc_final: 0.7978 (mp0) REVERT: B 417 ASN cc_start: 0.8827 (t0) cc_final: 0.8447 (t0) outliers start: 29 outliers final: 22 residues processed: 128 average time/residue: 0.1822 time to fit residues: 32.3067 Evaluate side-chains 130 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 472 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6702 Z= 0.194 Angle : 0.596 6.635 9110 Z= 0.315 Chirality : 0.044 0.193 964 Planarity : 0.004 0.047 1172 Dihedral : 5.086 38.124 984 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 4.03 % Allowed : 19.42 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.12 (0.29), residues: 787 helix: 0.79 (0.25), residues: 413 sheet: 0.44 (0.77), residues: 42 loop : -1.25 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 473 HIS 0.005 0.001 HIS A 374 PHE 0.033 0.002 PHE B 375 TYR 0.013 0.002 TYR A 199 ARG 0.003 0.001 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.8667 (t-100) cc_final: 0.8310 (t60) REVERT: A 243 TYR cc_start: 0.8816 (t80) cc_final: 0.8573 (t80) REVERT: A 249 MET cc_start: 0.8366 (mtm) cc_final: 0.8107 (mtp) REVERT: A 287 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6523 (pm20) REVERT: A 323 MET cc_start: 0.8531 (mmm) cc_final: 0.6898 (mmm) REVERT: A 361 CYS cc_start: 0.5440 (OUTLIER) cc_final: 0.5131 (p) REVERT: A 366 MET cc_start: 0.8611 (ppp) cc_final: 0.7835 (ppp) REVERT: A 376 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7672 (tpt) REVERT: A 441 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8370 (ttpp) REVERT: A 471 ASP cc_start: 0.8960 (p0) cc_final: 0.8729 (p0) REVERT: B 406 GLU cc_start: 0.8305 (mp0) cc_final: 0.8022 (mp0) REVERT: B 420 ASP cc_start: 0.6875 (m-30) cc_final: 0.6662 (m-30) outliers start: 28 outliers final: 18 residues processed: 132 average time/residue: 0.1649 time to fit residues: 29.7732 Evaluate side-chains 121 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 472 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.0770 chunk 22 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 472 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6702 Z= 0.187 Angle : 0.599 6.634 9110 Z= 0.315 Chirality : 0.044 0.204 964 Planarity : 0.004 0.046 1172 Dihedral : 5.000 37.198 984 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 4.03 % Allowed : 20.43 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.02 (0.29), residues: 787 helix: 0.91 (0.25), residues: 407 sheet: 0.30 (0.79), residues: 40 loop : -1.18 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 473 HIS 0.004 0.001 HIS A 374 PHE 0.016 0.001 PHE B 490 TYR 0.016 0.001 TYR A 199 ARG 0.008 0.001 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.8698 (t-100) cc_final: 0.8341 (t60) REVERT: A 243 TYR cc_start: 0.8805 (t80) cc_final: 0.8599 (t80) REVERT: A 249 MET cc_start: 0.8407 (mtm) cc_final: 0.8180 (mtp) REVERT: A 287 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6707 (pm20) REVERT: A 323 MET cc_start: 0.8514 (mmm) cc_final: 0.6868 (mmm) REVERT: A 361 CYS cc_start: 0.5492 (OUTLIER) cc_final: 0.4880 (p) REVERT: A 366 MET cc_start: 0.8566 (ppp) cc_final: 0.7809 (ppp) REVERT: A 376 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7675 (tpt) REVERT: A 406 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8587 (mm-30) REVERT: A 441 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8432 (ttpp) REVERT: A 461 TRP cc_start: 0.9078 (m-10) cc_final: 0.8763 (m-10) REVERT: A 480 MET cc_start: 0.8831 (mtt) cc_final: 0.8593 (mtm) REVERT: A 560 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8793 (mt) REVERT: B 406 GLU cc_start: 0.8427 (mp0) cc_final: 0.8121 (mp0) outliers start: 28 outliers final: 20 residues processed: 122 average time/residue: 0.1496 time to fit residues: 25.5852 Evaluate side-chains 126 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 42 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN B 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.6739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6702 Z= 0.183 Angle : 0.610 10.688 9110 Z= 0.318 Chirality : 0.044 0.188 964 Planarity : 0.004 0.046 1172 Dihedral : 4.996 36.377 984 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 3.74 % Allowed : 21.87 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.01 (0.29), residues: 787 helix: 1.03 (0.26), residues: 400 sheet: 0.15 (0.79), residues: 41 loop : -1.24 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 473 HIS 0.005 0.001 HIS A 374 PHE 0.019 0.001 PHE A 592 TYR 0.020 0.002 TYR A 199 ARG 0.007 0.001 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.9045 (m110) cc_final: 0.8761 (m-40) REVERT: A 152 MET cc_start: 0.7603 (mmm) cc_final: 0.7142 (mmt) REVERT: A 163 TRP cc_start: 0.8703 (t-100) cc_final: 0.8353 (t60) REVERT: A 243 TYR cc_start: 0.8866 (t80) cc_final: 0.8647 (t80) REVERT: A 249 MET cc_start: 0.8443 (mtm) cc_final: 0.8220 (mtp) REVERT: A 306 ARG cc_start: 0.8518 (ttp-170) cc_final: 0.8220 (ttp-170) REVERT: A 323 MET cc_start: 0.8538 (mmm) cc_final: 0.7177 (mmm) REVERT: A 361 CYS cc_start: 0.5341 (OUTLIER) cc_final: 0.4839 (p) REVERT: A 366 MET cc_start: 0.8522 (ppp) cc_final: 0.7775 (ppp) REVERT: A 376 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7548 (tpt) REVERT: A 406 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8595 (mm-30) REVERT: A 441 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8587 (ttpp) REVERT: A 461 TRP cc_start: 0.9083 (m-10) cc_final: 0.8798 (m-10) REVERT: A 512 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8209 (t80) REVERT: A 560 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8788 (mt) REVERT: B 406 GLU cc_start: 0.8374 (mp0) cc_final: 0.8069 (mp0) outliers start: 26 outliers final: 17 residues processed: 124 average time/residue: 0.1570 time to fit residues: 26.7459 Evaluate side-chains 122 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS 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: 1.9990 chunk 21 optimal weight: 0.2980 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.6937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6702 Z= 0.176 Angle : 0.604 10.164 9110 Z= 0.315 Chirality : 0.043 0.189 964 Planarity : 0.004 0.045 1172 Dihedral : 4.820 34.728 984 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 3.45 % Allowed : 23.17 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.19 (0.30), residues: 787 helix: 1.26 (0.26), residues: 392 sheet: 0.26 (0.80), residues: 41 loop : -1.21 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 473 HIS 0.004 0.001 HIS A 374 PHE 0.033 0.001 PHE B 375 TYR 0.023 0.001 TYR A 199 ARG 0.002 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8005 (ppp) cc_final: 0.7539 (ppp) REVERT: A 121 ASN cc_start: 0.9016 (m110) cc_final: 0.8700 (m-40) REVERT: A 163 TRP cc_start: 0.8713 (t-100) cc_final: 0.8396 (t60) REVERT: A 234 LYS cc_start: 0.9431 (ptmm) cc_final: 0.9025 (pttp) REVERT: A 243 TYR cc_start: 0.8871 (t80) cc_final: 0.8627 (t80) REVERT: A 270 MET cc_start: 0.6978 (tpt) cc_final: 0.6718 (tpt) REVERT: A 287 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6759 (pm20) REVERT: A 306 ARG cc_start: 0.8521 (ttp-170) cc_final: 0.8166 (ttp-170) REVERT: A 323 MET cc_start: 0.8514 (mmm) cc_final: 0.7153 (mmm) REVERT: A 361 CYS cc_start: 0.5270 (OUTLIER) cc_final: 0.4805 (p) REVERT: A 366 MET cc_start: 0.8390 (ppp) cc_final: 0.7740 (ppp) REVERT: A 376 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7517 (tpt) REVERT: A 406 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8615 (mm-30) REVERT: A 461 TRP cc_start: 0.9044 (m-10) cc_final: 0.8760 (m-10) REVERT: A 512 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8174 (t80) REVERT: A 572 ASN cc_start: 0.8842 (t0) cc_final: 0.8362 (p0) REVERT: B 406 GLU cc_start: 0.8388 (mp0) cc_final: 0.8099 (mp0) outliers start: 24 outliers final: 15 residues processed: 122 average time/residue: 0.1642 time to fit residues: 27.7285 Evaluate side-chains 118 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 0.0050 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.0370 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.6973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 6702 Z= 0.289 Angle : 1.019 59.200 9110 Z= 0.590 Chirality : 0.049 0.503 964 Planarity : 0.005 0.046 1172 Dihedral : 4.823 34.714 984 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.93 % Rotamer: Outliers : 2.88 % Allowed : 23.60 % Favored : 73.53 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.50 % 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: 0.21 (0.30), residues: 787 helix: 1.27 (0.26), residues: 392 sheet: 0.28 (0.80), residues: 41 loop : -1.19 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 473 HIS 0.004 0.001 HIS A 374 PHE 0.032 0.001 PHE B 375 TYR 0.024 0.001 TYR A 199 ARG 0.009 0.001 ARG B 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7994 (ppp) cc_final: 0.7534 (ppp) REVERT: A 121 ASN cc_start: 0.9012 (m110) cc_final: 0.8696 (m-40) REVERT: A 163 TRP cc_start: 0.8718 (t-100) cc_final: 0.8395 (t60) REVERT: A 234 LYS cc_start: 0.9432 (ptmm) cc_final: 0.9026 (pttp) REVERT: A 243 TYR cc_start: 0.8872 (t80) cc_final: 0.8629 (t80) REVERT: A 270 MET cc_start: 0.6959 (tpt) cc_final: 0.6710 (tpt) REVERT: A 306 ARG cc_start: 0.8522 (ttp-170) cc_final: 0.8221 (ttp-170) REVERT: A 323 MET cc_start: 0.8507 (mmm) cc_final: 0.7545 (mmm) REVERT: A 361 CYS cc_start: 0.5274 (OUTLIER) cc_final: 0.4804 (p) REVERT: A 366 MET cc_start: 0.8372 (ppp) cc_final: 0.7734 (ppp) REVERT: A 406 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8612 (mm-30) REVERT: A 461 TRP cc_start: 0.9047 (m-10) cc_final: 0.8763 (m-10) REVERT: A 512 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8177 (t80) REVERT: A 572 ASN cc_start: 0.8839 (t0) cc_final: 0.8355 (p0) REVERT: B 406 GLU cc_start: 0.8381 (mp0) cc_final: 0.8098 (mp0) outliers start: 20 outliers final: 16 residues processed: 113 average time/residue: 0.1564 time to fit residues: 25.0896 Evaluate side-chains 118 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 5.9990 chunk 61 optimal weight: 0.0070 chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.0030 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 41 optimal weight: 0.0010 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.137566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.110585 restraints weight = 16224.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.113594 restraints weight = 9362.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.115539 restraints weight = 6456.162| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.6970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 6702 Z= 0.289 Angle : 1.019 59.200 9110 Z= 0.590 Chirality : 0.049 0.503 964 Planarity : 0.005 0.047 1172 Dihedral : 4.823 34.714 984 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.93 % Rotamer: Outliers : 2.73 % Allowed : 23.88 % Favored : 73.38 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.50 % 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: 0.21 (0.30), residues: 787 helix: 1.27 (0.26), residues: 392 sheet: 0.28 (0.80), residues: 41 loop : -1.19 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 473 HIS 0.004 0.001 HIS A 374 PHE 0.032 0.001 PHE B 375 TYR 0.024 0.001 TYR A 199 ARG 0.009 0.001 ARG B 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1820.86 seconds wall clock time: 33 minutes 12.06 seconds (1992.06 seconds total)