Starting phenix.real_space_refine on Wed Jun 26 03:39:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf1_39207/06_2024/8yf1_39207_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf1_39207/06_2024/8yf1_39207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf1_39207/06_2024/8yf1_39207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf1_39207/06_2024/8yf1_39207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf1_39207/06_2024/8yf1_39207_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf1_39207/06_2024/8yf1_39207_updated.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.090 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 5998 2.51 5 N 1520 2.21 5 O 1599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 442": "OE1" <-> "OE2" Residue "B PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 675": "OE1" <-> "OE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 9187 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4505 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 13, 'TRANS': 553} Chain breaks: 1 Chain: "A" Number of atoms: 4652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4652 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 15, 'TRANS': 573} Chain breaks: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'VLX': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'VLX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.32, per 1000 atoms: 0.58 Number of scatterers: 9187 At special positions: 0 Unit cell: (118.364, 101.588, 129.548, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1599 8.00 N 1520 7.00 C 5998 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: 3.67 Conformation dependent library (CDL) restraints added in 1.4 seconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 0 sheets defined 64.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'B' and resid 134 through 159 removed outlier: 3.989A pdb=" N GLU B 146 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 188 removed outlier: 3.907A pdb=" N ALA B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 227 removed outlier: 5.667A pdb=" N GLY B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU B 209 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 250 Processing helix chain 'B' and resid 255 through 283 removed outlier: 4.265A pdb=" N GLY B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE B 273 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Proline residue: B 274 - end of helix removed outlier: 4.122A pdb=" N PHE B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 293 No H-bonds generated for 'chain 'B' and resid 290 through 293' Processing helix chain 'B' and resid 295 through 314 removed outlier: 3.506A pdb=" N MET B 301 " --> pdb=" O MET B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 332 through 350 Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 368 through 383 removed outlier: 4.452A pdb=" N ARG B 383 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 398 removed outlier: 4.835A pdb=" N VAL B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR B 395 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS B 396 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS B 398 " --> pdb=" O VAL B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 438 removed outlier: 3.649A pdb=" N CYS B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 483 removed outlier: 3.920A pdb=" N SER B 458 " --> pdb=" O TRP B 454 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE B 459 " --> pdb=" O PHE B 455 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N SER B 460 " --> pdb=" O THR B 456 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR B 461 " --> pdb=" O MET B 457 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Proline residue: B 469 - end of helix Processing helix chain 'B' and resid 563 through 565 No H-bonds generated for 'chain 'B' and resid 563 through 565' Processing helix chain 'B' and resid 597 through 621 removed outlier: 4.093A pdb=" N LEU B 609 " --> pdb=" O THR B 605 " (cutoff:3.500A) Proline residue: B 610 - end of helix removed outlier: 4.045A pdb=" N VAL B 614 " --> pdb=" O PRO B 610 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 615 " --> pdb=" O GLY B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 643 Processing helix chain 'B' and resid 650 through 676 removed outlier: 4.263A pdb=" N VAL B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 707 removed outlier: 5.435A pdb=" N THR B 683 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR B 684 " --> pdb=" O LYS B 681 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 699 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 704 " --> pdb=" O ILE B 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 159 Processing helix chain 'A' and resid 163 through 188 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 203 through 229 removed outlier: 4.006A pdb=" N ASP A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 Processing helix chain 'A' and resid 255 through 270 removed outlier: 3.586A pdb=" N VAL A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 283 removed outlier: 3.876A pdb=" N SER A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR A 279 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 314 removed outlier: 4.450A pdb=" N GLY A 290 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TRP A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N CYS A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N MET A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE A 299 " --> pdb=" O TRP A 295 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TRP A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 340 Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 368 through 384 removed outlier: 4.719A pdb=" N ALA A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 393 through 401 Processing helix chain 'A' and resid 420 through 439 removed outlier: 3.872A pdb=" N PHE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 465 removed outlier: 4.199A pdb=" N PHE A 459 " --> pdb=" O PHE A 455 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY A 463 " --> pdb=" O PHE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 482 Processing helix chain 'A' and resid 592 through 621 removed outlier: 3.511A pdb=" N TYR A 595 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N MET A 596 " --> pdb=" O GLY A 593 " (cutoff:3.500A) Proline residue: A 610 - end of helix removed outlier: 3.661A pdb=" N MET A 619 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP A 620 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 642 Processing helix chain 'A' and resid 649 through 676 removed outlier: 3.808A pdb=" N GLY A 660 " --> pdb=" O CYS A 656 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 706 Processing helix chain 'A' and resid 714 through 726 515 hydrogen bonds defined for protein. 1329 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: 2.41 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1413 1.31 - 1.43: 2875 1.43 - 1.56: 5042 1.56 - 1.69: 0 1.69 - 1.82: 112 Bond restraints: 9442 Sorted by residual: bond pdb=" C6 VLX A 801 " pdb=" N1 VLX A 801 " ideal model delta sigma weight residual 1.351 1.518 -0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" C6 VLX B 801 " pdb=" N1 VLX B 801 " ideal model delta sigma weight residual 1.351 1.507 -0.156 2.00e-02 2.50e+03 6.06e+01 bond pdb=" C9 VLX A 801 " pdb=" N2 VLX A 801 " ideal model delta sigma weight residual 1.339 1.461 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C9 VLX B 801 " pdb=" N2 VLX B 801 " ideal model delta sigma weight residual 1.339 1.457 -0.118 2.00e-02 2.50e+03 3.51e+01 bond pdb=" CA GLU B 282 " pdb=" C GLU B 282 " ideal model delta sigma weight residual 1.523 1.450 0.073 1.41e-02 5.03e+03 2.67e+01 ... (remaining 9437 not shown) Histogram of bond angle deviations from ideal: 97.76 - 105.02: 129 105.02 - 112.27: 4542 112.27 - 119.53: 3112 119.53 - 126.78: 4837 126.78 - 134.04: 151 Bond angle restraints: 12771 Sorted by residual: angle pdb=" N GLU B 282 " pdb=" CA GLU B 282 " pdb=" C GLU B 282 " ideal model delta sigma weight residual 113.16 107.70 5.46 1.24e+00 6.50e-01 1.94e+01 angle pdb=" N THR A 684 " pdb=" CA THR A 684 " pdb=" CB THR A 684 " ideal model delta sigma weight residual 109.82 115.87 -6.05 1.52e+00 4.33e-01 1.58e+01 angle pdb=" N HIS A 378 " pdb=" CA HIS A 378 " pdb=" CB HIS A 378 " ideal model delta sigma weight residual 110.16 115.06 -4.90 1.48e+00 4.57e-01 1.10e+01 angle pdb=" O THR A 683 " pdb=" C THR A 683 " pdb=" N THR A 684 " ideal model delta sigma weight residual 122.15 118.38 3.77 1.14e+00 7.69e-01 1.10e+01 angle pdb=" CA THR A 683 " pdb=" C THR A 683 " pdb=" N THR A 684 " ideal model delta sigma weight residual 117.39 121.36 -3.97 1.24e+00 6.50e-01 1.03e+01 ... (remaining 12766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 5008 23.85 - 47.71: 354 47.71 - 71.56: 26 71.56 - 95.41: 10 95.41 - 119.27: 4 Dihedral angle restraints: 5402 sinusoidal: 2116 harmonic: 3286 Sorted by residual: dihedral pdb=" C6 VLX B 801 " pdb=" C5 VLX B 801 " pdb=" N1 VLX B 801 " pdb=" C8 VLX B 801 " ideal model delta sinusoidal sigma weight residual -168.88 -49.61 -119.27 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" C6 VLX B 801 " pdb=" C5 VLX B 801 " pdb=" N1 VLX B 801 " pdb=" C9 VLX B 801 " ideal model delta sinusoidal sigma weight residual 68.19 -177.87 -113.94 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" C2 VLX B 801 " pdb=" C5 VLX B 801 " pdb=" N1 VLX B 801 " pdb=" C8 VLX B 801 " ideal model delta sinusoidal sigma weight residual 26.74 132.70 -105.96 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 5399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1217 0.065 - 0.130: 146 0.130 - 0.194: 4 0.194 - 0.259: 2 0.259 - 0.324: 2 Chirality restraints: 1371 Sorted by residual: chirality pdb=" C5 VLX B 801 " pdb=" C8 VLX B 801 " pdb=" C9 VLX B 801 " pdb=" N1 VLX B 801 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" C1 VLX A 801 " pdb=" C2 VLX A 801 " pdb=" C3 VLX A 801 " pdb=" C4 VLX A 801 " both_signs ideal model delta sigma weight residual False -2.61 -2.88 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C1 VLX B 801 " pdb=" C2 VLX B 801 " pdb=" C3 VLX B 801 " pdb=" C4 VLX B 801 " both_signs ideal model delta sigma weight residual False -2.61 -2.86 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1368 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 281 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C SER B 281 " 0.066 2.00e-02 2.50e+03 pdb=" O SER B 281 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU B 282 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 354 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 355 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 315 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO A 316 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 316 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 316 " -0.029 5.00e-02 4.00e+02 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1051 2.75 - 3.29: 9507 3.29 - 3.82: 15794 3.82 - 4.36: 17225 4.36 - 4.90: 29916 Nonbonded interactions: 73493 Sorted by model distance: nonbonded pdb=" OH TYR B 279 " pdb=" O PRO B 355 " model vdw 2.211 2.440 nonbonded pdb=" OG SER A 238 " pdb=" O GLY A 268 " model vdw 2.230 2.440 nonbonded pdb=" OG SER A 542 " pdb=" OG1 THR A 588 " model vdw 2.255 2.440 nonbonded pdb=" O MET B 619 " pdb=" NH1 ARG B 626 " model vdw 2.276 2.520 nonbonded pdb=" O CYS A 549 " pdb=" OG SER A 569 " model vdw 2.279 2.440 ... (remaining 73488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 133 through 709 or resid 801)) selection = (chain 'B' and (resid 133 through 402 or resid 416 through 709 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 4.550 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.620 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 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 : 0.005 0.167 9442 Z= 0.315 Angle : 0.641 9.246 12771 Z= 0.330 Chirality : 0.043 0.324 1371 Planarity : 0.004 0.054 1605 Dihedral : 15.672 119.268 3308 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.86 (0.26), residues: 1148 helix: 0.98 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -0.02 (0.34), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 666 HIS 0.013 0.001 HIS A 396 PHE 0.032 0.001 PHE B 640 TYR 0.017 0.001 TYR B 595 ARG 0.007 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.843 Fit side-chains REVERT: B 450 MET cc_start: 0.6702 (tpp) cc_final: 0.6298 (tpp) REVERT: A 206 MET cc_start: 0.7032 (tmm) cc_final: 0.6580 (tmm) REVERT: A 344 SER cc_start: 0.9049 (p) cc_final: 0.8840 (p) REVERT: A 382 MET cc_start: 0.6213 (ttm) cc_final: 0.5867 (ttm) REVERT: A 420 TRP cc_start: 0.7028 (m100) cc_final: 0.6704 (m100) REVERT: A 596 MET cc_start: 0.6916 (tpt) cc_final: 0.6461 (tpt) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1919 time to fit residues: 38.1455 Evaluate side-chains 124 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 20.0000 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 29 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 34 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 ASN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9442 Z= 0.186 Angle : 0.540 6.909 12771 Z= 0.282 Chirality : 0.039 0.330 1371 Planarity : 0.004 0.042 1605 Dihedral : 7.585 96.320 1292 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.24 % Allowed : 8.06 % Favored : 90.70 % 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: 0.77 (0.26), residues: 1148 helix: 0.91 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.06 (0.34), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 333 HIS 0.016 0.001 HIS A 378 PHE 0.025 0.001 PHE B 640 TYR 0.011 0.001 TYR A 212 ARG 0.002 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 0.951 Fit side-chains REVERT: B 619 MET cc_start: 0.7470 (ptm) cc_final: 0.7205 (ptm) REVERT: B 657 LEU cc_start: 0.7588 (mp) cc_final: 0.7335 (mp) REVERT: A 382 MET cc_start: 0.6147 (ttm) cc_final: 0.5564 (ttm) REVERT: A 420 TRP cc_start: 0.7082 (m100) cc_final: 0.6711 (m100) REVERT: A 457 MET cc_start: 0.7927 (tmm) cc_final: 0.7708 (tmm) REVERT: A 596 MET cc_start: 0.7113 (tpt) cc_final: 0.6678 (tpt) outliers start: 12 outliers final: 10 residues processed: 127 average time/residue: 0.1828 time to fit residues: 34.1510 Evaluate side-chains 125 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 711 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 0.2980 chunk 70 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 92 optimal weight: 40.0000 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9442 Z= 0.203 Angle : 0.529 6.744 12771 Z= 0.274 Chirality : 0.038 0.149 1371 Planarity : 0.004 0.035 1605 Dihedral : 6.347 65.014 1292 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.86 % Allowed : 11.88 % Favored : 86.26 % 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: 0.74 (0.26), residues: 1148 helix: 0.87 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.06 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 467 HIS 0.011 0.001 HIS A 378 PHE 0.025 0.001 PHE B 640 TYR 0.011 0.001 TYR A 279 ARG 0.002 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.988 Fit side-chains REVERT: B 324 MET cc_start: 0.2936 (pmm) cc_final: 0.2612 (pmm) REVERT: A 142 ARG cc_start: 0.6175 (ppt170) cc_final: 0.5760 (ppt170) REVERT: A 275 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7970 (mt) REVERT: A 382 MET cc_start: 0.6254 (ttm) cc_final: 0.5477 (ttm) REVERT: A 420 TRP cc_start: 0.7228 (m100) cc_final: 0.6717 (m100) outliers start: 18 outliers final: 15 residues processed: 130 average time/residue: 0.1876 time to fit residues: 35.3466 Evaluate side-chains 133 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 596 MET Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 720 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 11 optimal weight: 0.0170 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 0.0670 chunk 29 optimal weight: 4.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9442 Z= 0.148 Angle : 0.507 9.882 12771 Z= 0.257 Chirality : 0.037 0.127 1371 Planarity : 0.004 0.033 1605 Dihedral : 5.814 55.220 1292 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.45 % Allowed : 14.46 % Favored : 84.09 % 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: 0.91 (0.26), residues: 1148 helix: 1.01 (0.19), residues: 751 sheet: None (None), residues: 0 loop : -0.01 (0.34), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 300 HIS 0.010 0.001 HIS A 378 PHE 0.022 0.001 PHE B 640 TYR 0.008 0.001 TYR B 462 ARG 0.003 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 0.892 Fit side-chains REVERT: B 324 MET cc_start: 0.2931 (pmm) cc_final: 0.2608 (pmm) REVERT: B 619 MET cc_start: 0.7363 (ptm) cc_final: 0.7152 (ptm) REVERT: B 675 GLU cc_start: 0.7091 (pt0) cc_final: 0.6726 (tp30) REVERT: A 142 ARG cc_start: 0.6195 (ppt170) cc_final: 0.5774 (ppt170) REVERT: A 206 MET cc_start: 0.6907 (tmm) cc_final: 0.6403 (tmm) REVERT: A 275 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7893 (mt) REVERT: A 382 MET cc_start: 0.6260 (ttm) cc_final: 0.5313 (ttm) REVERT: A 420 TRP cc_start: 0.7244 (m100) cc_final: 0.6719 (m100) outliers start: 14 outliers final: 12 residues processed: 128 average time/residue: 0.1746 time to fit residues: 33.0520 Evaluate side-chains 132 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 596 MET Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 720 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.1980 chunk 62 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 98 optimal weight: 0.0980 chunk 27 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 ASN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9442 Z= 0.191 Angle : 0.531 9.024 12771 Z= 0.270 Chirality : 0.038 0.139 1371 Planarity : 0.004 0.035 1605 Dihedral : 5.258 42.285 1292 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.07 % Allowed : 14.88 % Favored : 83.06 % 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: 0.90 (0.26), residues: 1148 helix: 1.00 (0.19), residues: 748 sheet: None (None), residues: 0 loop : 0.01 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 467 HIS 0.010 0.001 HIS A 378 PHE 0.023 0.001 PHE B 640 TYR 0.015 0.001 TYR A 598 ARG 0.003 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 0.943 Fit side-chains REVERT: A 142 ARG cc_start: 0.6246 (ppt170) cc_final: 0.5707 (ppt170) REVERT: A 275 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7967 (mt) REVERT: A 382 MET cc_start: 0.6162 (ttm) cc_final: 0.5134 (ttm) REVERT: A 420 TRP cc_start: 0.7250 (m100) cc_final: 0.6712 (m100) REVERT: A 462 TYR cc_start: 0.7210 (t80) cc_final: 0.6983 (t80) REVERT: A 596 MET cc_start: 0.7237 (tpt) cc_final: 0.6192 (tpp) REVERT: A 618 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7685 (tp) outliers start: 20 outliers final: 16 residues processed: 127 average time/residue: 0.1907 time to fit residues: 35.0262 Evaluate side-chains 133 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 720 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 91 optimal weight: 0.0060 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9442 Z= 0.185 Angle : 0.539 9.468 12771 Z= 0.273 Chirality : 0.038 0.137 1371 Planarity : 0.004 0.035 1605 Dihedral : 4.962 37.999 1292 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.38 % Allowed : 15.70 % Favored : 81.92 % 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: 0.93 (0.26), residues: 1148 helix: 1.07 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -0.04 (0.34), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 300 HIS 0.009 0.001 HIS A 378 PHE 0.024 0.001 PHE B 640 TYR 0.010 0.001 TYR A 279 ARG 0.004 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 0.931 Fit side-chains REVERT: A 142 ARG cc_start: 0.6222 (ppt170) cc_final: 0.5690 (ppt170) REVERT: A 275 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7960 (mt) REVERT: A 420 TRP cc_start: 0.7239 (m100) cc_final: 0.6701 (m100) REVERT: A 596 MET cc_start: 0.7218 (tpt) cc_final: 0.6174 (tpp) REVERT: A 618 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7815 (tp) outliers start: 23 outliers final: 17 residues processed: 129 average time/residue: 0.1830 time to fit residues: 34.9275 Evaluate side-chains 134 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 596 MET Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 720 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.0770 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 40.0000 chunk 61 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9442 Z= 0.159 Angle : 0.518 9.468 12771 Z= 0.263 Chirality : 0.038 0.243 1371 Planarity : 0.004 0.033 1605 Dihedral : 4.590 33.828 1292 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.38 % Allowed : 16.74 % Favored : 80.89 % 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: 1.02 (0.26), residues: 1148 helix: 1.09 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.06 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 333 HIS 0.009 0.001 HIS A 378 PHE 0.021 0.001 PHE B 640 TYR 0.009 0.001 TYR B 462 ARG 0.004 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 0.910 Fit side-chains REVERT: B 450 MET cc_start: 0.6813 (tpp) cc_final: 0.6431 (tpp) REVERT: A 142 ARG cc_start: 0.6223 (ppt170) cc_final: 0.5702 (ppt170) REVERT: A 275 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7928 (mt) REVERT: A 382 MET cc_start: 0.5641 (ttm) cc_final: 0.4463 (ttm) REVERT: A 420 TRP cc_start: 0.7174 (m100) cc_final: 0.6680 (m100) REVERT: A 596 MET cc_start: 0.7230 (tpt) cc_final: 0.6206 (tpp) REVERT: A 618 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7972 (tp) outliers start: 23 outliers final: 18 residues processed: 132 average time/residue: 0.1763 time to fit residues: 34.4869 Evaluate side-chains 139 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 292 HIS Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 596 MET Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 720 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 HIS ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9442 Z= 0.258 Angle : 0.591 9.155 12771 Z= 0.301 Chirality : 0.041 0.285 1371 Planarity : 0.004 0.038 1605 Dihedral : 4.731 37.288 1292 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.48 % Allowed : 16.84 % Favored : 80.68 % 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: 0.77 (0.26), residues: 1148 helix: 0.94 (0.20), residues: 736 sheet: None (None), residues: 0 loop : -0.11 (0.34), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 467 HIS 0.009 0.001 HIS A 396 PHE 0.029 0.002 PHE B 640 TYR 0.015 0.001 TYR A 279 ARG 0.003 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 0.876 Fit side-chains REVERT: B 163 ARG cc_start: 0.5141 (tpp-160) cc_final: 0.4413 (tpp-160) REVERT: A 142 ARG cc_start: 0.6254 (ppt170) cc_final: 0.5716 (ppt170) REVERT: A 275 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7995 (mt) REVERT: A 346 PHE cc_start: 0.5292 (OUTLIER) cc_final: 0.4398 (m-10) REVERT: A 382 MET cc_start: 0.5958 (ttm) cc_final: 0.4479 (ttm) REVERT: A 420 TRP cc_start: 0.7174 (m100) cc_final: 0.6666 (m100) REVERT: A 596 MET cc_start: 0.7243 (tpt) cc_final: 0.6241 (tpp) REVERT: A 618 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7975 (tp) outliers start: 24 outliers final: 20 residues processed: 135 average time/residue: 0.1729 time to fit residues: 34.0241 Evaluate side-chains 142 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 292 HIS Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 596 MET Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 720 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.3980 chunk 102 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 61 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 67 optimal weight: 0.3980 chunk 108 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9442 Z= 0.159 Angle : 0.545 9.529 12771 Z= 0.274 Chirality : 0.039 0.281 1371 Planarity : 0.004 0.034 1605 Dihedral : 4.485 31.847 1292 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.27 % Allowed : 17.67 % Favored : 80.06 % 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: 0.93 (0.26), residues: 1148 helix: 1.07 (0.20), residues: 738 sheet: None (None), residues: 0 loop : -0.06 (0.34), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 333 HIS 0.018 0.001 HIS A 378 PHE 0.022 0.001 PHE B 640 TYR 0.009 0.001 TYR B 462 ARG 0.002 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 0.850 Fit side-chains REVERT: B 161 HIS cc_start: 0.7693 (t70) cc_final: 0.7368 (t-90) REVERT: B 613 ILE cc_start: 0.8180 (mp) cc_final: 0.7745 (mt) REVERT: A 142 ARG cc_start: 0.6230 (ppt170) cc_final: 0.5703 (ppt170) REVERT: A 275 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7908 (mt) REVERT: A 382 MET cc_start: 0.5624 (ttm) cc_final: 0.4201 (ttm) REVERT: A 420 TRP cc_start: 0.7164 (m100) cc_final: 0.6645 (m100) REVERT: A 596 MET cc_start: 0.7166 (tpt) cc_final: 0.6290 (tpp) REVERT: A 618 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7879 (tp) outliers start: 22 outliers final: 18 residues processed: 130 average time/residue: 0.1968 time to fit residues: 37.2069 Evaluate side-chains 138 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 596 MET Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 720 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 96 optimal weight: 0.0040 chunk 27 optimal weight: 10.0000 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9442 Z= 0.164 Angle : 0.544 8.962 12771 Z= 0.272 Chirality : 0.039 0.287 1371 Planarity : 0.004 0.039 1605 Dihedral : 4.271 29.950 1292 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.17 % Allowed : 17.98 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1148 helix: 1.11 (0.20), residues: 742 sheet: None (None), residues: 0 loop : 0.01 (0.34), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 300 HIS 0.017 0.001 HIS A 378 PHE 0.022 0.001 PHE B 640 TYR 0.009 0.001 TYR B 462 ARG 0.004 0.000 ARG B 289 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 0.954 Fit side-chains REVERT: B 161 HIS cc_start: 0.7545 (t70) cc_final: 0.7052 (t70) REVERT: B 613 ILE cc_start: 0.8131 (mp) cc_final: 0.7706 (mt) REVERT: A 206 MET cc_start: 0.6984 (tmm) cc_final: 0.6488 (tmm) REVERT: A 275 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7920 (mt) REVERT: A 420 TRP cc_start: 0.7156 (m100) cc_final: 0.6642 (m100) REVERT: A 596 MET cc_start: 0.7216 (tpt) cc_final: 0.6316 (tpp) REVERT: A 618 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8011 (tp) outliers start: 21 outliers final: 17 residues processed: 125 average time/residue: 0.1827 time to fit residues: 33.3295 Evaluate side-chains 133 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 596 MET Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 720 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.262648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.193484 restraints weight = 10408.034| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 3.60 r_work: 0.3849 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9442 Z= 0.305 Angle : 0.634 9.688 12771 Z= 0.321 Chirality : 0.043 0.284 1371 Planarity : 0.004 0.041 1605 Dihedral : 4.679 32.546 1292 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.48 % Allowed : 17.25 % Favored : 80.27 % 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: 0.59 (0.26), residues: 1148 helix: 0.74 (0.19), residues: 743 sheet: None (None), residues: 0 loop : -0.07 (0.34), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 467 HIS 0.017 0.001 HIS A 378 PHE 0.033 0.002 PHE B 640 TYR 0.017 0.001 TYR A 279 ARG 0.002 0.000 ARG B 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2128.82 seconds wall clock time: 38 minutes 22.16 seconds (2302.16 seconds total)