Starting phenix.real_space_refine on Fri Mar 15 07:44:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrj_14916/03_2024/7zrj_14916_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrj_14916/03_2024/7zrj_14916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrj_14916/03_2024/7zrj_14916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrj_14916/03_2024/7zrj_14916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrj_14916/03_2024/7zrj_14916_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrj_14916/03_2024/7zrj_14916_updated.pdb" } resolution = 3.7 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= 0.001 sd= 0.005 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 K 7 8.98 5 P 5 5.49 5 S 62 5.16 5 C 7120 2.51 5 N 1821 2.21 5 O 1994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 302": "OE1" <-> "OE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "B GLU 208": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11009 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5016 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 26, 'TRANS': 648} Chain: "A" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 206 Unusual residues: {' K': 6, 'CDL': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.67, per 1000 atoms: 0.61 Number of scatterers: 11009 At special positions: 0 Unit cell: (98.164, 112.332, 153.824, 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) K 7 19.00 S 62 16.00 P 5 15.00 O 1994 8.00 N 1821 7.00 C 7120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 4.96 Conformation dependent library (CDL) restraints added in 2.4 seconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 6 sheets defined 54.9% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 Proline residue: A 22 - end of helix removed outlier: 3.624A pdb=" N SER A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 50 removed outlier: 3.898A pdb=" N ARG A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 81 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 132 through 156 removed outlier: 3.576A pdb=" N GLN A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 219 through 227 removed outlier: 3.858A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.606A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 277 through 304 removed outlier: 4.023A pdb=" N LEU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.788A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 378 through 398 removed outlier: 4.164A pdb=" N MET A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 434 removed outlier: 4.650A pdb=" N LEU A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 464 Processing helix chain 'A' and resid 479 through 494 Processing helix chain 'A' and resid 497 through 509 removed outlier: 4.020A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 537 Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'C' and resid 4 through 18 Processing helix chain 'C' and resid 22 through 33 removed outlier: 3.535A pdb=" N TRP C 32 " --> pdb=" O VAL C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 38 No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 134 through 148 removed outlier: 3.910A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Proline residue: C 142 - end of helix Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'C' and resid 179 through 189 Processing helix chain 'D' and resid 6 through 24 Processing helix chain 'B' and resid 15 through 21 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 34 through 55 removed outlier: 4.200A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 96 Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 216 through 245 removed outlier: 4.403A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 273 through 285 removed outlier: 5.977A pdb=" N GLY B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 330 through 341 Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 398 through 407 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 496 through 508 Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 555 through 594 removed outlier: 4.297A pdb=" N LEU B 558 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE B 559 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 566 " --> pdb=" O HIS B 563 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET B 568 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B 573 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 582 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 584 " --> pdb=" O ALA B 581 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE B 591 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 604 removed outlier: 4.135A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 636 removed outlier: 3.782A pdb=" N ILE B 617 " --> pdb=" O PRO B 613 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU B 618 " --> pdb=" O ASP B 614 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 646 through 660 removed outlier: 4.372A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 679 Processing sheet with id= A, first strand: chain 'A' and resid 202 through 205 Processing sheet with id= B, first strand: chain 'C' and resid 42 through 44 removed outlier: 3.874A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 131 through 134 Processing sheet with id= D, first strand: chain 'B' and resid 287 through 289 Processing sheet with id= E, first strand: chain 'B' and resid 466 through 469 Processing sheet with id= F, first strand: chain 'B' and resid 393 through 396 524 hydrogen bonds defined for protein. 1443 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: 2.98 Time building geometry restraints manager: 5.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1859 1.32 - 1.45: 2669 1.45 - 1.57: 6548 1.57 - 1.69: 12 1.69 - 1.82: 112 Bond restraints: 11200 Sorted by residual: bond pdb=" OA3 CDL A 607 " pdb=" PA1 CDL A 607 " ideal model delta sigma weight residual 1.529 1.502 0.027 1.00e-02 1.00e+04 7.20e+00 bond pdb=" OA3 CDL A 608 " pdb=" PA1 CDL A 608 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.95e+00 bond pdb=" N ASP C 111 " pdb=" CA ASP C 111 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.31e-02 5.83e+03 6.86e+00 bond pdb=" OB3 CDL A 608 " pdb=" PB2 CDL A 608 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.27e+00 bond pdb=" OB3 CDL A 607 " pdb=" PB2 CDL A 607 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.11e+00 ... (remaining 11195 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.47: 261 105.47 - 112.62: 5884 112.62 - 119.77: 3801 119.77 - 126.92: 5117 126.92 - 134.07: 134 Bond angle restraints: 15197 Sorted by residual: angle pdb=" C GLY A 83 " pdb=" N GLN A 84 " pdb=" CA GLN A 84 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 angle pdb=" N GLU B 544 " pdb=" CA GLU B 544 " pdb=" CB GLU B 544 " ideal model delta sigma weight residual 110.28 117.15 -6.87 1.55e+00 4.16e-01 1.96e+01 angle pdb=" CA GLU B 544 " pdb=" CB GLU B 544 " pdb=" CG GLU B 544 " ideal model delta sigma weight residual 114.10 122.69 -8.59 2.00e+00 2.50e-01 1.84e+01 angle pdb=" CB MET A 227 " pdb=" CG MET A 227 " pdb=" SD MET A 227 " ideal model delta sigma weight residual 112.70 123.42 -10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" CA TYR A 381 " pdb=" CB TYR A 381 " pdb=" CG TYR A 381 " ideal model delta sigma weight residual 113.90 120.24 -6.34 1.80e+00 3.09e-01 1.24e+01 ... (remaining 15192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 5880 17.26 - 34.51: 636 34.51 - 51.77: 156 51.77 - 69.02: 45 69.02 - 86.28: 15 Dihedral angle restraints: 6732 sinusoidal: 2629 harmonic: 4103 Sorted by residual: dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 151.28 28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA PHE A 373 " pdb=" C PHE A 373 " pdb=" N GLY A 374 " pdb=" CA GLY A 374 " ideal model delta harmonic sigma weight residual -180.00 -159.42 -20.58 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ILE B 656 " pdb=" C ILE B 656 " pdb=" N TYR B 657 " pdb=" CA TYR B 657 " ideal model delta harmonic sigma weight residual -180.00 -160.57 -19.43 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 6729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1433 0.058 - 0.116: 332 0.116 - 0.174: 39 0.174 - 0.233: 3 0.233 - 0.291: 3 Chirality restraints: 1810 Sorted by residual: chirality pdb=" CG LEU A 170 " pdb=" CB LEU A 170 " pdb=" CD1 LEU A 170 " pdb=" CD2 LEU A 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB ILE B 386 " pdb=" CA ILE B 386 " pdb=" CG1 ILE B 386 " pdb=" CG2 ILE B 386 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB VAL C 175 " pdb=" CA VAL C 175 " pdb=" CG1 VAL C 175 " pdb=" CG2 VAL C 175 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1807 not shown) Planarity restraints: 1908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 153 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" CD GLU C 153 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLU C 153 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU C 153 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 116 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO C 117 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 117 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 117 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 133 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO C 134 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 134 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 134 " -0.031 5.00e-02 4.00e+02 ... (remaining 1905 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.77: 2051 2.77 - 3.36: 12954 3.36 - 3.96: 22017 3.96 - 4.55: 30200 4.55 - 5.14: 44848 Nonbonded interactions: 112070 Sorted by model distance: nonbonded pdb=" O ASP C 111 " pdb=" OD1 ASP C 111 " model vdw 2.179 3.040 nonbonded pdb=" O LEU A 541 " pdb=" OH TYR B 587 " model vdw 2.205 2.440 nonbonded pdb=" O THR A 248 " pdb=" OG1 THR A 251 " model vdw 2.268 2.440 nonbonded pdb=" O SER A 119 " pdb=" OG1 THR A 123 " model vdw 2.294 2.440 nonbonded pdb=" O PRO C 23 " pdb=" OG1 THR C 27 " model vdw 2.296 2.440 ... (remaining 112065 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=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: 0.760 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: 3.650 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 35.250 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 0.043 11200 Z= 0.258 Angle : 0.804 10.716 15197 Z= 0.406 Chirality : 0.049 0.291 1810 Planarity : 0.005 0.057 1908 Dihedral : 16.082 86.276 4096 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.20), residues: 1438 helix: -0.15 (0.17), residues: 859 sheet: -1.55 (0.79), residues: 35 loop : -1.80 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 115 HIS 0.002 0.001 HIS B 563 PHE 0.030 0.002 PHE C 34 TYR 0.029 0.002 TYR A 381 ARG 0.009 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.177 Fit side-chains REVERT: A 176 TRP cc_start: 0.7393 (m100) cc_final: 0.7135 (m100) REVERT: A 412 ARG cc_start: 0.6980 (mmt180) cc_final: 0.6656 (mmt180) REVERT: B 303 VAL cc_start: 0.8514 (t) cc_final: 0.8105 (t) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2041 time to fit residues: 49.9543 Evaluate side-chains 129 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 112 optimal weight: 0.3980 chunk 43 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 466 ASN A 467 ASN ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11200 Z= 0.208 Angle : 0.559 7.796 15197 Z= 0.282 Chirality : 0.040 0.167 1810 Planarity : 0.004 0.045 1908 Dihedral : 11.037 88.517 1714 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.88 % Allowed : 8.81 % Favored : 90.31 % 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: -0.48 (0.22), residues: 1438 helix: 0.58 (0.18), residues: 851 sheet: -1.07 (0.71), residues: 45 loop : -1.67 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 655 HIS 0.002 0.001 HIS A 451 PHE 0.014 0.001 PHE B 173 TYR 0.017 0.002 TYR A 458 ARG 0.005 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 1.308 Fit side-chains REVERT: A 176 TRP cc_start: 0.7505 (m100) cc_final: 0.7223 (m100) outliers start: 10 outliers final: 7 residues processed: 137 average time/residue: 0.2064 time to fit residues: 42.5583 Evaluate side-chains 127 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 526 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11200 Z= 0.214 Angle : 0.546 6.660 15197 Z= 0.271 Chirality : 0.040 0.148 1810 Planarity : 0.004 0.044 1908 Dihedral : 10.401 87.362 1714 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.59 % Allowed : 11.10 % Favored : 87.31 % 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 (0.22), residues: 1438 helix: 0.81 (0.18), residues: 853 sheet: -0.73 (0.73), residues: 45 loop : -1.53 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 115 HIS 0.003 0.001 HIS A 242 PHE 0.013 0.001 PHE B 173 TYR 0.016 0.002 TYR A 381 ARG 0.003 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.286 Fit side-chains REVERT: A 176 TRP cc_start: 0.7553 (m100) cc_final: 0.7261 (m100) REVERT: A 445 MET cc_start: 0.7491 (mmt) cc_final: 0.7012 (mmt) outliers start: 18 outliers final: 13 residues processed: 140 average time/residue: 0.2094 time to fit residues: 43.8962 Evaluate side-chains 131 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 626 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11200 Z= 0.296 Angle : 0.595 8.279 15197 Z= 0.296 Chirality : 0.042 0.198 1810 Planarity : 0.004 0.043 1908 Dihedral : 10.208 80.891 1714 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.82 % Allowed : 13.48 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.22), residues: 1438 helix: 0.82 (0.18), residues: 835 sheet: -0.41 (0.80), residues: 40 loop : -1.47 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 31 HIS 0.003 0.001 HIS B 563 PHE 0.018 0.001 PHE A 373 TYR 0.019 0.002 TYR A 458 ARG 0.004 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7586 (m100) cc_final: 0.7296 (m100) REVERT: A 436 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7949 (mtt) REVERT: A 445 MET cc_start: 0.8304 (mmt) cc_final: 0.7937 (mmt) REVERT: B 142 CYS cc_start: 0.7015 (p) cc_final: 0.6510 (p) REVERT: B 469 MET cc_start: 0.6834 (ttt) cc_final: 0.6503 (mtp) outliers start: 32 outliers final: 21 residues processed: 141 average time/residue: 0.2086 time to fit residues: 44.1647 Evaluate side-chains 133 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 603 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 0.0980 chunk 78 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11200 Z= 0.162 Angle : 0.531 8.446 15197 Z= 0.262 Chirality : 0.039 0.139 1810 Planarity : 0.004 0.043 1908 Dihedral : 9.664 82.161 1714 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.03 % Allowed : 15.42 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1438 helix: 1.01 (0.19), residues: 844 sheet: -0.61 (0.80), residues: 42 loop : -1.40 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 115 HIS 0.002 0.000 HIS A 242 PHE 0.012 0.001 PHE B 173 TYR 0.018 0.001 TYR A 381 ARG 0.003 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7471 (m100) cc_final: 0.7198 (m100) REVERT: A 187 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8824 (mm) REVERT: A 412 ARG cc_start: 0.7258 (mmt180) cc_final: 0.6980 (mmt180) REVERT: A 445 MET cc_start: 0.8154 (mmt) cc_final: 0.7758 (mmt) REVERT: B 469 MET cc_start: 0.6780 (ttt) cc_final: 0.6469 (mtp) outliers start: 23 outliers final: 11 residues processed: 142 average time/residue: 0.2240 time to fit residues: 47.6999 Evaluate side-chains 127 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 576 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 27 optimal weight: 0.0980 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 64 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 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 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11200 Z= 0.144 Angle : 0.516 9.089 15197 Z= 0.256 Chirality : 0.039 0.138 1810 Planarity : 0.004 0.043 1908 Dihedral : 9.208 82.091 1714 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.03 % Allowed : 15.86 % Favored : 82.11 % 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: 0.21 (0.23), residues: 1438 helix: 1.11 (0.19), residues: 848 sheet: -0.39 (0.82), residues: 42 loop : -1.36 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 115 HIS 0.002 0.000 HIS A 242 PHE 0.012 0.001 PHE B 173 TYR 0.018 0.001 TYR A 381 ARG 0.004 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7439 (m100) cc_final: 0.7155 (m100) REVERT: A 187 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8853 (mm) REVERT: A 445 MET cc_start: 0.8056 (mmt) cc_final: 0.7653 (mmt) outliers start: 23 outliers final: 12 residues processed: 143 average time/residue: 0.1977 time to fit residues: 42.4617 Evaluate side-chains 128 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 576 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 0.0870 chunk 101 optimal weight: 0.8980 chunk 116 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11200 Z= 0.147 Angle : 0.528 9.372 15197 Z= 0.257 Chirality : 0.039 0.137 1810 Planarity : 0.004 0.043 1908 Dihedral : 8.891 81.700 1714 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.29 % Allowed : 16.48 % Favored : 81.23 % 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: 0.27 (0.23), residues: 1438 helix: 1.17 (0.19), residues: 846 sheet: -0.69 (0.77), residues: 46 loop : -1.32 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 115 HIS 0.002 0.000 HIS A 242 PHE 0.011 0.001 PHE B 173 TYR 0.016 0.001 TYR A 381 ARG 0.004 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7428 (m100) cc_final: 0.7151 (m100) REVERT: A 183 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8391 (mm) REVERT: A 187 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8763 (mm) REVERT: A 397 MET cc_start: 0.8605 (mmm) cc_final: 0.7982 (mtt) REVERT: A 445 MET cc_start: 0.8041 (mmt) cc_final: 0.7618 (mmt) REVERT: B 383 MET cc_start: 0.5279 (ttt) cc_final: 0.4575 (tmm) outliers start: 26 outliers final: 17 residues processed: 145 average time/residue: 0.1988 time to fit residues: 43.4652 Evaluate side-chains 139 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 576 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 41 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11200 Z= 0.218 Angle : 0.561 9.695 15197 Z= 0.275 Chirality : 0.040 0.135 1810 Planarity : 0.004 0.042 1908 Dihedral : 8.957 78.728 1714 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.38 % Allowed : 16.83 % Favored : 80.79 % 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: 0.22 (0.23), residues: 1438 helix: 1.15 (0.19), residues: 843 sheet: -1.48 (0.69), residues: 59 loop : -1.27 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 115 HIS 0.003 0.001 HIS A 242 PHE 0.013 0.001 PHE B 173 TYR 0.016 0.001 TYR A 381 ARG 0.004 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7514 (m100) cc_final: 0.7222 (m100) REVERT: A 183 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8476 (mm) REVERT: A 187 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8805 (mm) REVERT: A 397 MET cc_start: 0.8830 (mmm) cc_final: 0.8106 (mtt) REVERT: A 445 MET cc_start: 0.8285 (mmt) cc_final: 0.7903 (mmt) REVERT: B 142 CYS cc_start: 0.7027 (p) cc_final: 0.6509 (p) REVERT: B 383 MET cc_start: 0.5286 (ttt) cc_final: 0.4571 (tmm) outliers start: 27 outliers final: 20 residues processed: 135 average time/residue: 0.2109 time to fit residues: 42.5079 Evaluate side-chains 137 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 576 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 100 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 127 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11200 Z= 0.157 Angle : 0.542 11.525 15197 Z= 0.263 Chirality : 0.039 0.172 1810 Planarity : 0.004 0.042 1908 Dihedral : 8.743 79.372 1714 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.03 % Allowed : 17.18 % Favored : 80.79 % 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: 0.32 (0.23), residues: 1438 helix: 1.19 (0.19), residues: 843 sheet: -0.62 (0.78), residues: 46 loop : -1.27 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 115 HIS 0.002 0.000 HIS A 242 PHE 0.012 0.001 PHE B 173 TYR 0.018 0.001 TYR A 381 ARG 0.004 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8309 (mp) cc_final: 0.7969 (mp) REVERT: A 176 TRP cc_start: 0.7411 (m100) cc_final: 0.7134 (m100) REVERT: A 183 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8336 (mm) REVERT: A 187 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8748 (mm) REVERT: A 397 MET cc_start: 0.8699 (mmm) cc_final: 0.8027 (mtt) REVERT: A 445 MET cc_start: 0.8141 (mmt) cc_final: 0.7798 (mmt) REVERT: B 31 TRP cc_start: 0.7552 (p-90) cc_final: 0.7302 (p-90) REVERT: B 383 MET cc_start: 0.5530 (ttt) cc_final: 0.4797 (tmm) outliers start: 23 outliers final: 17 residues processed: 134 average time/residue: 0.2034 time to fit residues: 41.0070 Evaluate side-chains 138 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 576 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11200 Z= 0.170 Angle : 0.551 12.154 15197 Z= 0.266 Chirality : 0.040 0.148 1810 Planarity : 0.004 0.042 1908 Dihedral : 8.670 78.491 1714 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.11 % Allowed : 17.18 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1438 helix: 1.25 (0.19), residues: 834 sheet: -1.45 (0.69), residues: 59 loop : -1.23 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 115 HIS 0.002 0.000 HIS A 242 PHE 0.012 0.001 PHE B 173 TYR 0.018 0.001 TYR A 381 ARG 0.004 0.000 ARG A 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8367 (mp) cc_final: 0.7981 (mp) REVERT: A 176 TRP cc_start: 0.7414 (m100) cc_final: 0.7132 (m100) REVERT: A 183 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8367 (mm) REVERT: A 187 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8746 (mm) REVERT: A 397 MET cc_start: 0.8715 (mmm) cc_final: 0.8042 (mtt) REVERT: A 445 MET cc_start: 0.8154 (mmt) cc_final: 0.7807 (mmt) REVERT: B 31 TRP cc_start: 0.7583 (p-90) cc_final: 0.7338 (p-90) REVERT: B 383 MET cc_start: 0.5472 (ttt) cc_final: 0.4787 (tmm) outliers start: 24 outliers final: 20 residues processed: 136 average time/residue: 0.2007 time to fit residues: 41.0109 Evaluate side-chains 141 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 576 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 113 optimal weight: 30.0000 chunk 47 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 99 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.120479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.093654 restraints weight = 21120.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.092821 restraints weight = 13643.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.093455 restraints weight = 11340.061| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11200 Z= 0.156 Angle : 0.553 11.483 15197 Z= 0.267 Chirality : 0.040 0.378 1810 Planarity : 0.004 0.042 1908 Dihedral : 8.543 78.471 1714 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.03 % Allowed : 17.53 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.23), residues: 1438 helix: 1.25 (0.19), residues: 834 sheet: -0.58 (0.78), residues: 46 loop : -1.30 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 115 HIS 0.002 0.000 HIS A 242 PHE 0.011 0.001 PHE B 173 TYR 0.018 0.001 TYR A 381 ARG 0.004 0.000 ARG A 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2051.17 seconds wall clock time: 38 minutes 1.80 seconds (2281.80 seconds total)