Starting phenix.real_space_refine on Fri Jul 19 04:59:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgw_37517/07_2024/8wgw_37517_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgw_37517/07_2024/8wgw_37517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgw_37517/07_2024/8wgw_37517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgw_37517/07_2024/8wgw_37517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgw_37517/07_2024/8wgw_37517_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wgw_37517/07_2024/8wgw_37517_neut.cif" } resolution = 2.9 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= -0.005 sd= 0.079 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4199 2.51 5 N 1084 2.21 5 O 1243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 428": "OD1" <-> "OD2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 543": "OD1" <-> "OD2" Residue "B GLU 571": "OE1" <-> "OE2" Residue "B ASP 597": "OD1" <-> "OD2" Residue "B TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6564 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1589 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 198, 1578 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Conformer: "B" Number of residues, atoms: 198, 1578 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} bond proxies already assigned to first conformer: 1613 Chain: "B" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 493 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 493 " occ=0.50 Time building chain proxies: 5.56, per 1000 atoms: 0.85 Number of scatterers: 6564 At special positions: 0 Unit cell: (82.016, 84.812, 119.296, 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 1243 8.00 N 1084 7.00 C 4199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 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 BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG B 701 " - " ASN B 322 " " NAG B 702 " - " ASN B 432 " " NAG B 703 " - " ASN B 103 " " NAG B 704 " - " ASN B 90 " " NAG B 705 " - " ASN B 53 " " NAG C 1 " - " ASN B 546 " Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.3 seconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1498 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 51.6% alpha, 6.9% 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 337 through 342 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.588A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.436A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'B' and resid 20 through 53 removed outlier: 3.690A pdb=" N HIS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 81 removed outlier: 3.613A pdb=" N GLN B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.533A pdb=" N SER B 106 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 109 through 129 Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.670A pdb=" N ASN B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 172 Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 176 through 194 removed outlier: 3.602A pdb=" N VAL B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 220 through 227 removed outlier: 3.709A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 303 through 319 Processing helix chain 'B' and resid 324 through 331 removed outlier: 3.777A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 386 Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.654A pdb=" N ALA B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.702A pdb=" N SER B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 444 removed outlier: 3.968A pdb=" N GLU B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 436 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 466 Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 472 through 482 Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 505 through 509 removed outlier: 4.084A pdb=" N ASP B 509 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 532 removed outlier: 4.258A pdb=" N TYR B 516 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.584A pdb=" N LYS B 541 " --> pdb=" O PRO B 538 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS B 542 " --> pdb=" O LEU B 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 538 through 542' Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.794A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.757A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 131 through 132 removed outlier: 3.820A pdb=" N LEU B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 262 through 263 removed outlier: 5.928A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 352 removed outlier: 6.052A pdb=" N ASP B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) 289 hydrogen bonds defined for protein. 831 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: 1.80 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2091 1.34 - 1.46: 1586 1.46 - 1.58: 3012 1.58 - 1.69: 1 1.69 - 1.81: 58 Bond restraints: 6748 Sorted by residual: bond pdb=" CB PRO B 289 " pdb=" CG PRO B 289 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.06e+01 bond pdb=" C1 NAG B 704 " pdb=" O5 NAG B 704 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C1 NAG B 703 " pdb=" O5 NAG B 703 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.70e+00 bond pdb=" CA VAL B 339 " pdb=" CB VAL B 339 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.08e-02 8.57e+03 1.60e+00 bond pdb=" C2 NAG B 703 " pdb=" N2 NAG B 703 " ideal model delta sigma weight residual 1.439 1.464 -0.025 2.00e-02 2.50e+03 1.52e+00 ... (remaining 6743 not shown) Histogram of bond angle deviations from ideal: 96.94 - 104.47: 113 104.47 - 112.01: 3180 112.01 - 119.54: 2377 119.54 - 127.08: 3397 127.08 - 134.61: 104 Bond angle restraints: 9171 Sorted by residual: angle pdb=" CA PRO B 289 " pdb=" N PRO B 289 " pdb=" CD PRO B 289 " ideal model delta sigma weight residual 112.00 100.06 11.94 1.40e+00 5.10e-01 7.27e+01 angle pdb=" N PRO B 289 " pdb=" CD PRO B 289 " pdb=" CG PRO B 289 " ideal model delta sigma weight residual 103.20 96.94 6.26 1.50e+00 4.44e-01 1.74e+01 angle pdb=" N VAL A 367 " pdb=" CA VAL A 367 " pdb=" C VAL A 367 " ideal model delta sigma weight residual 112.29 108.65 3.64 9.40e-01 1.13e+00 1.50e+01 angle pdb=" N GLY B 466 " pdb=" CA GLY B 466 " pdb=" C GLY B 466 " ideal model delta sigma weight residual 113.18 120.66 -7.48 2.37e+00 1.78e-01 9.96e+00 angle pdb=" N PRO B 289 " pdb=" CA PRO B 289 " pdb=" C PRO B 289 " ideal model delta sigma weight residual 111.03 115.70 -4.67 1.78e+00 3.16e-01 6.87e+00 ... (remaining 9166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 3683 21.43 - 42.85: 286 42.85 - 64.28: 52 64.28 - 85.70: 9 85.70 - 107.13: 42 Dihedral angle restraints: 4072 sinusoidal: 1737 harmonic: 2335 Sorted by residual: dihedral pdb=" CA ASN B 338 " pdb=" C ASN B 338 " pdb=" N VAL B 339 " pdb=" CA VAL B 339 " ideal model delta harmonic sigma weight residual 180.00 158.50 21.50 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" C2 NAG B 701 " pdb=" C3 NAG B 701 " pdb=" C4 NAG B 701 " pdb=" O4 NAG B 701 " ideal model delta sinusoidal sigma weight residual 175.11 67.98 107.13 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C2 NAG B 701 " pdb=" C3 NAG B 701 " pdb=" C4 NAG B 701 " pdb=" C5 NAG B 701 " ideal model delta sinusoidal sigma weight residual 53.78 -53.19 106.97 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 4069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 726 0.045 - 0.090: 195 0.090 - 0.135: 55 0.135 - 0.180: 2 0.180 - 0.225: 2 Chirality restraints: 980 Sorted by residual: chirality pdb=" CG LEU B 267 " pdb=" CB LEU B 267 " pdb=" CD1 LEU B 267 " pdb=" CD2 LEU B 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C1 NAG B 702 " pdb=" ND2 ASN B 432 " pdb=" C2 NAG B 702 " pdb=" O5 NAG B 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" C2 NAG B 703 " pdb=" C1 NAG B 703 " pdb=" C3 NAG B 703 " pdb=" N2 NAG B 703 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.18 2.00e-01 2.50e+01 7.85e-01 ... (remaining 977 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 288 " -0.050 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO B 289 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 289 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 289 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 425 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.32e+00 pdb=" N PRO B 426 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 426 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 426 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 478 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 479 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.024 5.00e-02 4.00e+02 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 204 2.71 - 3.26: 6682 3.26 - 3.81: 10938 3.81 - 4.35: 13988 4.35 - 4.90: 23629 Nonbonded interactions: 55441 Sorted by model distance: nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.167 2.440 nonbonded pdb=" OE2 GLU B 166 " pdb=" OG SER B 170 " model vdw 2.167 2.440 nonbonded pdb=" O SER A 359 " pdb=" OG1 THR A 523 " model vdw 2.178 2.440 nonbonded pdb=" OG SER B 331 " pdb=" O ILE B 358 " model vdw 2.244 2.440 nonbonded pdb=" OD1 ASP B 382 " pdb=" OH TYR B 385 " model vdw 2.256 2.440 ... (remaining 55436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.50 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: 4.220 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.150 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 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 0.163 6748 Z= 0.244 Angle : 0.592 11.938 9171 Z= 0.303 Chirality : 0.044 0.225 980 Planarity : 0.005 0.070 1179 Dihedral : 19.741 107.128 2571 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.14 % Allowed : 0.00 % 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: -0.16 (0.30), residues: 793 helix: 0.73 (0.27), residues: 372 sheet: -0.07 (0.73), residues: 57 loop : -0.96 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 566 HIS 0.004 0.001 HIS B 374 PHE 0.011 0.001 PHE B 369 TYR 0.022 0.001 TYR B 381 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.776 Fit side-chains REVERT: A 444 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7801 (mtpm) REVERT: B 98 GLN cc_start: 0.7706 (tt0) cc_final: 0.7471 (tt0) REVERT: B 227 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7206 (mt-10) REVERT: B 383 MET cc_start: 0.9016 (mtp) cc_final: 0.8801 (mtp) REVERT: B 597 ASP cc_start: 0.7476 (m-30) cc_final: 0.7135 (t0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 1.2645 time to fit residues: 158.2012 Evaluate side-chains 90 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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: 3.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 70 optimal weight: 0.0870 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 506 GLN B 58 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN B 325 GLN B 578 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6748 Z= 0.425 Angle : 0.704 9.854 9171 Z= 0.343 Chirality : 0.049 0.269 980 Planarity : 0.005 0.042 1179 Dihedral : 14.222 84.340 1034 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.87 % Allowed : 10.47 % Favored : 86.66 % 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: -0.39 (0.30), residues: 793 helix: 0.52 (0.27), residues: 386 sheet: -0.15 (0.73), residues: 57 loop : -1.12 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 477 HIS 0.008 0.001 HIS B 374 PHE 0.021 0.002 PHE B 400 TYR 0.051 0.002 TYR B 381 ARG 0.003 0.000 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.746 Fit side-chains REVERT: A 420 ASP cc_start: 0.8512 (m-30) cc_final: 0.8148 (m-30) REVERT: A 444 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7866 (mtpm) REVERT: B 98 GLN cc_start: 0.7935 (tt0) cc_final: 0.7721 (tt0) REVERT: B 479 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7362 (mt-10) REVERT: B 597 ASP cc_start: 0.7581 (m-30) cc_final: 0.7224 (t0) outliers start: 19 outliers final: 12 residues processed: 101 average time/residue: 1.1873 time to fit residues: 127.3588 Evaluate side-chains 101 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 401 HIS 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: 1.9990 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN B 34 HIS B 58 ASN B 60 GLN B 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6748 Z= 0.215 Angle : 0.591 9.728 9171 Z= 0.284 Chirality : 0.044 0.259 980 Planarity : 0.004 0.043 1179 Dihedral : 10.144 76.952 1034 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.30 % Allowed : 13.49 % Favored : 84.22 % 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: -0.16 (0.30), residues: 793 helix: 0.77 (0.27), residues: 377 sheet: -0.22 (0.74), residues: 57 loop : -0.99 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 566 HIS 0.005 0.001 HIS B 374 PHE 0.011 0.001 PHE B 327 TYR 0.022 0.001 TYR B 385 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.729 Fit side-chains REVERT: A 420 ASP cc_start: 0.8446 (m-30) cc_final: 0.8076 (m-30) REVERT: A 444 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7822 (mtpm) REVERT: A 471 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6896 (mm-30) REVERT: B 479 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7313 (mt-10) REVERT: B 571 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: B 597 ASP cc_start: 0.7516 (m-30) cc_final: 0.7218 (t0) outliers start: 15 outliers final: 9 residues processed: 107 average time/residue: 1.1156 time to fit residues: 126.4213 Evaluate side-chains 103 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 571 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 42 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 474 GLN B 58 ASN B 60 GLN B 159 ASN B 325 GLN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6748 Z= 0.237 Angle : 0.589 9.731 9171 Z= 0.286 Chirality : 0.044 0.270 980 Planarity : 0.004 0.045 1179 Dihedral : 8.970 70.165 1034 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.59 % Allowed : 14.06 % Favored : 82.35 % 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: -0.19 (0.30), residues: 793 helix: 0.71 (0.27), residues: 381 sheet: -0.23 (0.73), residues: 57 loop : -0.99 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 165 HIS 0.006 0.001 HIS B 374 PHE 0.010 0.001 PHE B 369 TYR 0.021 0.002 TYR B 385 ARG 0.001 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 0.643 Fit side-chains REVERT: A 420 ASP cc_start: 0.8467 (m-30) cc_final: 0.8120 (m-30) REVERT: A 444 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7841 (mtpm) REVERT: B 63 ASN cc_start: 0.8120 (m110) cc_final: 0.7834 (m110) REVERT: B 383 MET cc_start: 0.9149 (mtp) cc_final: 0.8822 (mtp) REVERT: B 571 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: B 597 ASP cc_start: 0.7498 (m-30) cc_final: 0.7199 (t0) outliers start: 24 outliers final: 13 residues processed: 112 average time/residue: 0.9802 time to fit residues: 116.9611 Evaluate side-chains 104 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 571 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.5980 chunk 56 optimal weight: 0.1980 chunk 31 optimal weight: 6.9990 chunk 64 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN B 58 ASN B 60 GLN B 159 ASN B 325 GLN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6748 Z= 0.170 Angle : 0.552 9.648 9171 Z= 0.269 Chirality : 0.042 0.254 980 Planarity : 0.004 0.047 1179 Dihedral : 8.068 61.988 1034 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.87 % Allowed : 16.36 % Favored : 80.77 % 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: -0.04 (0.31), residues: 793 helix: 0.85 (0.28), residues: 378 sheet: -0.23 (0.73), residues: 57 loop : -0.90 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 165 HIS 0.004 0.001 HIS B 374 PHE 0.011 0.001 PHE B 327 TYR 0.018 0.001 TYR B 385 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.803 Fit side-chains REVERT: A 444 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7815 (mtpm) REVERT: B 63 ASN cc_start: 0.8129 (m110) cc_final: 0.7841 (m110) REVERT: B 142 LEU cc_start: 0.7728 (mp) cc_final: 0.6955 (mt) REVERT: B 597 ASP cc_start: 0.7391 (m-30) cc_final: 0.7111 (t0) outliers start: 19 outliers final: 14 residues processed: 111 average time/residue: 1.1084 time to fit residues: 130.0921 Evaluate side-chains 103 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 0.0980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 506 GLN B 58 ASN B 60 GLN B 159 ASN B 325 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6748 Z= 0.222 Angle : 0.579 9.647 9171 Z= 0.282 Chirality : 0.043 0.250 980 Planarity : 0.004 0.049 1179 Dihedral : 7.808 58.724 1034 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.30 % Allowed : 15.93 % Favored : 80.77 % 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: -0.00 (0.31), residues: 793 helix: 0.84 (0.27), residues: 380 sheet: -0.05 (0.74), residues: 57 loop : -0.87 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 165 HIS 0.005 0.001 HIS B 374 PHE 0.011 0.001 PHE B 315 TYR 0.019 0.001 TYR B 385 ARG 0.002 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.716 Fit side-chains REVERT: A 428 ASP cc_start: 0.7881 (p0) cc_final: 0.7623 (p0) REVERT: A 444 LYS cc_start: 0.8155 (mtpt) cc_final: 0.7831 (mtpm) REVERT: A 471 GLU cc_start: 0.7331 (mm-30) cc_final: 0.7033 (mm-30) REVERT: B 63 ASN cc_start: 0.8131 (m110) cc_final: 0.7842 (m110) REVERT: B 171 GLU cc_start: 0.7107 (tt0) cc_final: 0.6820 (tt0) REVERT: B 571 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: B 597 ASP cc_start: 0.7423 (m-30) cc_final: 0.7128 (t0) outliers start: 22 outliers final: 13 residues processed: 106 average time/residue: 1.0520 time to fit residues: 118.2195 Evaluate side-chains 104 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 571 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 0.0670 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 44 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 506 GLN B 60 GLN B 159 ASN B 325 GLN B 522 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6748 Z= 0.202 Angle : 0.557 9.626 9171 Z= 0.273 Chirality : 0.042 0.251 980 Planarity : 0.004 0.049 1179 Dihedral : 7.324 57.313 1034 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.73 % Allowed : 16.50 % Favored : 79.77 % 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: 0.08 (0.31), residues: 793 helix: 0.93 (0.27), residues: 379 sheet: -0.04 (0.74), residues: 57 loop : -0.84 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 165 HIS 0.005 0.001 HIS B 374 PHE 0.010 0.001 PHE B 315 TYR 0.018 0.001 TYR B 385 ARG 0.002 0.000 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 0.727 Fit side-chains REVERT: A 428 ASP cc_start: 0.7873 (p0) cc_final: 0.7609 (p0) REVERT: A 444 LYS cc_start: 0.8152 (mtpt) cc_final: 0.7830 (mtpm) REVERT: B 63 ASN cc_start: 0.8134 (m110) cc_final: 0.7846 (m110) REVERT: B 150 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6391 (mt-10) REVERT: B 171 GLU cc_start: 0.7046 (tt0) cc_final: 0.6793 (tt0) REVERT: B 597 ASP cc_start: 0.7426 (m-30) cc_final: 0.7151 (t0) outliers start: 25 outliers final: 17 residues processed: 109 average time/residue: 1.0093 time to fit residues: 116.7817 Evaluate side-chains 107 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 506 GLN B 159 ASN B 325 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6748 Z= 0.250 Angle : 0.587 9.644 9171 Z= 0.288 Chirality : 0.043 0.250 980 Planarity : 0.004 0.049 1179 Dihedral : 7.072 57.636 1034 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.02 % Allowed : 15.78 % Favored : 80.20 % 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: 0.04 (0.31), residues: 793 helix: 0.86 (0.27), residues: 381 sheet: -0.05 (0.74), residues: 57 loop : -0.83 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 165 HIS 0.006 0.001 HIS B 374 PHE 0.010 0.001 PHE B 315 TYR 0.019 0.002 TYR B 385 ARG 0.002 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 0.730 Fit side-chains REVERT: A 420 ASP cc_start: 0.8418 (m-30) cc_final: 0.8033 (m-30) REVERT: A 428 ASP cc_start: 0.7888 (p0) cc_final: 0.7622 (p0) REVERT: A 444 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7824 (mtpm) REVERT: A 471 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7052 (mm-30) REVERT: B 63 ASN cc_start: 0.8096 (m110) cc_final: 0.7803 (m110) REVERT: B 171 GLU cc_start: 0.7067 (tt0) cc_final: 0.6832 (tt0) REVERT: B 571 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: B 597 ASP cc_start: 0.7387 (m-30) cc_final: 0.7079 (t0) outliers start: 27 outliers final: 17 residues processed: 106 average time/residue: 1.0729 time to fit residues: 121.0022 Evaluate side-chains 107 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 571 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 9.9990 chunk 55 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN B 159 ASN B 325 GLN B 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6748 Z= 0.223 Angle : 0.567 9.652 9171 Z= 0.279 Chirality : 0.043 0.251 980 Planarity : 0.004 0.049 1179 Dihedral : 6.635 57.608 1034 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.44 % Allowed : 16.21 % Favored : 80.34 % 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: 0.09 (0.31), residues: 793 helix: 0.92 (0.27), residues: 379 sheet: -0.08 (0.74), residues: 57 loop : -0.81 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 165 HIS 0.005 0.001 HIS B 374 PHE 0.010 0.001 PHE B 315 TYR 0.019 0.001 TYR B 385 ARG 0.002 0.000 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 89 time to evaluate : 0.695 Fit side-chains REVERT: A 428 ASP cc_start: 0.7884 (p0) cc_final: 0.7612 (p0) REVERT: A 444 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7817 (mtpm) REVERT: B 63 ASN cc_start: 0.8087 (m110) cc_final: 0.7795 (m110) REVERT: B 571 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: B 597 ASP cc_start: 0.7393 (m-30) cc_final: 0.7103 (t0) outliers start: 23 outliers final: 19 residues processed: 101 average time/residue: 0.9834 time to fit residues: 105.6020 Evaluate side-chains 108 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 571 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN B 159 ASN B 175 GLN B 325 GLN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6748 Z= 0.237 Angle : 0.569 9.660 9171 Z= 0.282 Chirality : 0.043 0.251 980 Planarity : 0.004 0.049 1179 Dihedral : 6.295 57.717 1034 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.44 % Allowed : 16.36 % Favored : 80.20 % 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: 0.02 (0.31), residues: 793 helix: 0.86 (0.27), residues: 381 sheet: -0.10 (0.74), residues: 57 loop : -0.86 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 165 HIS 0.006 0.001 HIS B 374 PHE 0.010 0.001 PHE B 315 TYR 0.019 0.002 TYR B 385 ARG 0.002 0.000 ARG B 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 89 time to evaluate : 0.730 Fit side-chains REVERT: A 386 LYS cc_start: 0.5775 (OUTLIER) cc_final: 0.5461 (tppt) REVERT: A 428 ASP cc_start: 0.7886 (p0) cc_final: 0.7624 (p0) REVERT: A 444 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7813 (mtpm) REVERT: A 471 GLU cc_start: 0.7239 (mm-30) cc_final: 0.7018 (mm-30) REVERT: B 63 ASN cc_start: 0.8101 (m110) cc_final: 0.7800 (m110) REVERT: B 571 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: B 597 ASP cc_start: 0.7394 (m-30) cc_final: 0.7103 (t0) outliers start: 23 outliers final: 19 residues processed: 100 average time/residue: 1.0944 time to fit residues: 116.3123 Evaluate side-chains 109 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 571 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.0030 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN B 159 ASN B 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.152006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122046 restraints weight = 14438.223| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 4.19 r_work: 0.3144 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6748 Z= 0.211 Angle : 0.553 9.651 9171 Z= 0.274 Chirality : 0.042 0.251 980 Planarity : 0.004 0.049 1179 Dihedral : 6.030 57.565 1034 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.59 % Allowed : 16.50 % Favored : 79.91 % 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: 0.04 (0.31), residues: 793 helix: 0.89 (0.27), residues: 381 sheet: -0.12 (0.74), residues: 57 loop : -0.86 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 566 HIS 0.005 0.001 HIS B 374 PHE 0.010 0.001 PHE B 315 TYR 0.018 0.001 TYR B 385 ARG 0.002 0.000 ARG B 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2814.18 seconds wall clock time: 50 minutes 39.97 seconds (3039.97 seconds total)