Starting phenix.real_space_refine on Fri Jul 19 23:21:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf1_39207/07_2024/8yf1_39207.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf1_39207/07_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_39207/07_2024/8yf1_39207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf1_39207/07_2024/8yf1_39207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf1_39207/07_2024/8yf1_39207.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yf1_39207/07_2024/8yf1_39207.cif" } 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-5388/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: 5.79, per 1000 atoms: 0.63 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: 3.87 Conformation dependent library (CDL) restraints added in 1.7 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... Secondary structure from input PDB file: 49 helices and 2 sheets defined 70.6% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'B' and resid 133 through 160 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) removed outlier: 3.891A pdb=" N GLY B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 189 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 202 through 226 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) Processing helix chain 'B' and resid 231 through 251 removed outlier: 3.510A pdb=" N LEU B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 271 removed outlier: 4.265A pdb=" N GLY B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 282 Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 295 through 315 removed outlier: 3.904A pdb=" N PHE B 299 " --> pdb=" O TRP B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.987A pdb=" N SER B 321 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 322 " --> pdb=" O GLY B 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 322' Processing helix chain 'B' and resid 332 through 341 removed outlier: 3.556A pdb=" N ALA B 341 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 357 through 365 removed outlier: 3.746A pdb=" N PHE B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 382 Processing helix chain 'B' and resid 388 through 399 removed outlier: 3.619A pdb=" N PHE B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) 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 439 removed outlier: 3.649A pdb=" N CYS B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 Processing helix chain 'B' and resid 458 through 484 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 562 through 566 removed outlier: 3.516A pdb=" N LYS B 565 " --> pdb=" O PHE B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 609 removed outlier: 4.093A pdb=" N LEU B 609 " --> pdb=" O THR B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 622 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 625 through 644 Processing helix chain 'B' and resid 649 through 677 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) removed outlier: 3.574A pdb=" N TYR B 677 " --> pdb=" O THR B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 680 No H-bonds generated for 'chain 'B' and resid 678 through 680' Processing helix chain 'B' and resid 681 through 708 removed outlier: 3.507A pdb=" N ALA B 685 " --> pdb=" O LYS B 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 160 Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.999A pdb=" N LYS A 195 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 230 removed outlier: 4.261A pdb=" N MET A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) 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 230 through 251 Processing helix chain 'A' and resid 254 through 271 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 272 through 281 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) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 285 through 294 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) Processing helix chain 'A' and resid 296 through 315 removed outlier: 3.734A pdb=" N TRP A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 341 Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.797A pdb=" N THR A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.534A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 386 through 391 Processing helix chain 'A' and resid 392 through 402 Processing helix chain 'A' and resid 419 through 438 Processing helix chain 'A' and resid 445 through 466 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 466 through 483 Processing helix chain 'A' and resid 591 through 593 No H-bonds generated for 'chain 'A' and resid 591 through 593' Processing helix chain 'A' and resid 594 through 620 Proline residue: A 610 - end of helix removed outlier: 3.871A pdb=" N ASP A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 643 Processing helix chain 'A' and resid 648 through 677 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) removed outlier: 3.742A pdb=" N TYR A 677 " --> pdb=" O THR A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 707 Processing helix chain 'A' and resid 713 through 727 Processing sheet with id=AA1, first strand: chain 'B' and resid 535 through 536 removed outlier: 3.722A pdb=" N PHE B 536 " --> pdb=" O VAL B 555 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 521 through 522 removed outlier: 6.574A pdb=" N LEU A 521 " --> pdb=" O SER A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 566 hydrogen bonds defined for protein. 1683 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: 2.57 Time building geometry restraints manager: 4.25 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: 1048 2.75 - 3.29: 9430 3.29 - 3.82: 15768 3.82 - 4.36: 17142 4.36 - 4.90: 29901 Nonbonded interactions: 73289 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 73284 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 28.580 Find NCS groups from input model: 0.490 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.660 ------------------------------------------------------------------------------- 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= 0.312 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 : 1.523 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: 0.1883 time to fit residues: 38.5536 Evaluate side-chains 124 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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: 0.5980 chunk 47 optimal weight: 0.4980 chunk 29 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6058 moved from start: 0.0698 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= 0.165 Angle : 0.531 6.914 12771 Z= 0.273 Chirality : 0.039 0.366 1371 Planarity : 0.003 0.044 1605 Dihedral : 7.605 95.552 1292 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.93 % Allowed : 8.88 % Favored : 90.19 % 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: 1.21 (0.26), residues: 1148 helix: 1.37 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -0.15 (0.34), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.011 0.001 HIS A 396 PHE 0.030 0.001 PHE B 640 TYR 0.009 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 135 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 0.992 Fit side-chains REVERT: B 163 ARG cc_start: 0.4838 (tpp-160) cc_final: 0.4172 (tpp-160) REVERT: B 657 LEU cc_start: 0.7565 (mp) cc_final: 0.7300 (mp) REVERT: A 382 MET cc_start: 0.5879 (ttm) cc_final: 0.5209 (ttm) REVERT: A 420 TRP cc_start: 0.7010 (m100) cc_final: 0.6694 (m100) REVERT: A 596 MET cc_start: 0.6847 (tpt) cc_final: 0.6470 (tpt) outliers start: 9 outliers final: 8 residues processed: 128 average time/residue: 0.1874 time to fit residues: 35.0095 Evaluate side-chains 123 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.7980 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 0.0770 chunk 92 optimal weight: 10.0000 chunk 102 optimal weight: 0.0570 chunk 35 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 overall best weight: 1.1058 ------------------------------------------------------------------------------- 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: 0.6137 moved from start: 0.0955 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= 0.217 Angle : 0.553 6.818 12771 Z= 0.284 Chirality : 0.039 0.157 1371 Planarity : 0.003 0.041 1605 Dihedral : 6.179 58.769 1292 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.86 % Allowed : 12.19 % Favored : 85.95 % 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: 1.23 (0.26), residues: 1148 helix: 1.38 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -0.13 (0.34), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 166 HIS 0.011 0.001 HIS A 378 PHE 0.033 0.001 PHE B 640 TYR 0.018 0.001 TYR A 212 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 148 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.018 Fit side-chains REVERT: B 163 ARG cc_start: 0.4981 (tpp-160) cc_final: 0.4278 (tpp-160) REVERT: B 301 MET cc_start: 0.8312 (tpp) cc_final: 0.8096 (mmt) REVERT: B 619 MET cc_start: 0.7510 (ptm) cc_final: 0.7279 (ptm) REVERT: A 142 ARG cc_start: 0.6194 (ppt170) cc_final: 0.5727 (ppt170) REVERT: A 275 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7875 (mt) REVERT: A 382 MET cc_start: 0.6119 (ttm) cc_final: 0.5444 (ttm) REVERT: A 420 TRP cc_start: 0.7124 (m100) cc_final: 0.6675 (m100) REVERT: A 596 MET cc_start: 0.6982 (tpt) cc_final: 0.6605 (tpt) outliers start: 18 outliers final: 14 residues processed: 136 average time/residue: 0.1851 time to fit residues: 36.9900 Evaluate side-chains 135 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 275 ILE 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 644 PHE 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: 0.7980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.6104 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9442 Z= 0.174 Angle : 0.526 7.341 12771 Z= 0.268 Chirality : 0.038 0.134 1371 Planarity : 0.003 0.039 1605 Dihedral : 5.915 51.728 1292 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.76 % Allowed : 14.57 % Favored : 83.68 % 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: 1.39 (0.26), residues: 1148 helix: 1.50 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.12 (0.35), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.011 0.001 HIS A 378 PHE 0.031 0.001 PHE B 640 TYR 0.010 0.001 TYR A 279 ARG 0.002 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 144 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 0.903 Fit side-chains REVERT: B 163 ARG cc_start: 0.5036 (tpp-160) cc_final: 0.4247 (tpp-160) REVERT: B 301 MET cc_start: 0.8293 (tpp) cc_final: 0.8066 (mmt) REVERT: A 142 ARG cc_start: 0.6155 (ppt170) cc_final: 0.5706 (ppt170) REVERT: A 275 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7934 (mt) REVERT: A 382 MET cc_start: 0.6133 (ttm) cc_final: 0.5348 (ttm) REVERT: A 420 TRP cc_start: 0.7191 (m100) cc_final: 0.6706 (m100) REVERT: A 596 MET cc_start: 0.6902 (tpt) cc_final: 0.6554 (tpt) outliers start: 17 outliers final: 15 residues processed: 133 average time/residue: 0.1864 time to fit residues: 36.7422 Evaluate side-chains 137 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 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 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 651 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 94 optimal weight: 40.0000 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.6165 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9442 Z= 0.238 Angle : 0.566 8.166 12771 Z= 0.288 Chirality : 0.039 0.147 1371 Planarity : 0.003 0.041 1605 Dihedral : 5.576 49.602 1292 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.07 % Allowed : 15.91 % Favored : 82.02 % 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: 1.27 (0.26), residues: 1148 helix: 1.42 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.16 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 467 HIS 0.012 0.001 HIS A 378 PHE 0.034 0.001 PHE B 640 TYR 0.013 0.001 TYR A 279 ARG 0.005 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 145 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.028 Fit side-chains REVERT: B 161 HIS cc_start: 0.7451 (t70) cc_final: 0.7066 (t-90) REVERT: B 163 ARG cc_start: 0.5212 (tpp-160) cc_final: 0.4526 (ttm170) REVERT: A 142 ARG cc_start: 0.6245 (ppt170) cc_final: 0.5745 (ppt170) REVERT: A 275 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7942 (mt) REVERT: A 420 TRP cc_start: 0.7218 (m100) cc_final: 0.6682 (m100) REVERT: A 596 MET cc_start: 0.6994 (tpt) cc_final: 0.6644 (tpt) outliers start: 20 outliers final: 14 residues processed: 134 average time/residue: 0.1874 time to fit residues: 36.7269 Evaluate side-chains 136 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 99 optimal weight: 30.0000 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 ASN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN A 331 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9442 Z= 0.400 Angle : 0.710 9.051 12771 Z= 0.365 Chirality : 0.045 0.175 1371 Planarity : 0.004 0.052 1605 Dihedral : 5.865 54.138 1292 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.79 % Allowed : 18.29 % Favored : 78.93 % 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: 0.60 (0.25), residues: 1148 helix: 0.82 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -0.25 (0.35), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 467 HIS 0.015 0.002 HIS A 378 PHE 0.041 0.002 PHE B 640 TYR 0.016 0.002 TYR A 279 ARG 0.005 0.001 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 151 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 0.849 Fit side-chains REVERT: B 161 HIS cc_start: 0.7909 (t70) cc_final: 0.7471 (t70) REVERT: B 328 TYR cc_start: 0.5040 (m-80) cc_final: 0.4796 (m-80) REVERT: A 142 ARG cc_start: 0.6097 (ppt170) cc_final: 0.5606 (ppt170) REVERT: A 275 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7848 (mt) REVERT: A 346 PHE cc_start: 0.5448 (OUTLIER) cc_final: 0.4559 (m-10) REVERT: A 382 MET cc_start: 0.5629 (ttm) cc_final: 0.4476 (ttm) REVERT: A 420 TRP cc_start: 0.7250 (m100) cc_final: 0.6609 (m100) REVERT: A 464 LEU cc_start: 0.8667 (tp) cc_final: 0.8464 (tp) REVERT: A 596 MET cc_start: 0.7259 (tpt) cc_final: 0.6938 (tpt) REVERT: A 622 ILE cc_start: 0.7787 (mt) cc_final: 0.7579 (mt) outliers start: 27 outliers final: 19 residues processed: 140 average time/residue: 0.1728 time to fit residues: 35.8201 Evaluate side-chains 140 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 600 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 655 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 339 VAL Chi-restraints excluded: chain A residue 346 PHE 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 720 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.0970 chunk 12 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 67 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 503 ASN B 612 ASN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.1523 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= 0.170 Angle : 0.553 9.951 12771 Z= 0.280 Chirality : 0.038 0.249 1371 Planarity : 0.003 0.039 1605 Dihedral : 5.218 41.890 1292 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.38 % Allowed : 19.32 % Favored : 78.31 % 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: 1.24 (0.26), residues: 1148 helix: 1.39 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.15 (0.35), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 333 HIS 0.012 0.001 HIS A 378 PHE 0.030 0.001 PHE B 640 TYR 0.011 0.001 TYR B 461 ARG 0.005 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 : 0.919 Fit side-chains REVERT: B 163 ARG cc_start: 0.5201 (tpp-160) cc_final: 0.4669 (ttm170) REVERT: B 328 TYR cc_start: 0.4958 (m-80) cc_final: 0.4725 (m-80) REVERT: B 382 MET cc_start: 0.4708 (ttt) cc_final: 0.3893 (ptt) REVERT: B 389 GLU cc_start: 0.7176 (tt0) cc_final: 0.6722 (tt0) REVERT: B 613 ILE cc_start: 0.8246 (mp) cc_final: 0.7861 (mt) REVERT: A 142 ARG cc_start: 0.6250 (ppt170) cc_final: 0.5750 (ppt170) REVERT: A 275 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7932 (mt) REVERT: A 382 MET cc_start: 0.5466 (ttm) cc_final: 0.4203 (ttm) REVERT: A 420 TRP cc_start: 0.7251 (m100) cc_final: 0.6601 (m100) REVERT: A 596 MET cc_start: 0.6855 (tpt) cc_final: 0.6568 (tpt) outliers start: 23 outliers final: 17 residues processed: 137 average time/residue: 0.1796 time to fit residues: 36.3141 Evaluate side-chains 135 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 331 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 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 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 720 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 0.1980 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 503 ASN ** 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: 0.6148 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9442 Z= 0.189 Angle : 0.566 10.197 12771 Z= 0.282 Chirality : 0.039 0.227 1371 Planarity : 0.003 0.038 1605 Dihedral : 4.912 37.389 1292 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.69 % Allowed : 19.42 % Favored : 77.89 % 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: 1.30 (0.26), residues: 1148 helix: 1.45 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.16 (0.35), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 333 HIS 0.012 0.001 HIS A 378 PHE 0.032 0.001 PHE B 640 TYR 0.010 0.001 TYR B 462 ARG 0.005 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 142 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 0.937 Fit side-chains REVERT: B 382 MET cc_start: 0.4874 (ttt) cc_final: 0.3934 (ptt) REVERT: B 389 GLU cc_start: 0.7159 (tt0) cc_final: 0.6691 (tt0) REVERT: B 613 ILE cc_start: 0.8256 (mp) cc_final: 0.7887 (mt) REVERT: A 142 ARG cc_start: 0.6255 (ppt170) cc_final: 0.5759 (ppt170) REVERT: A 275 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7932 (mt) REVERT: A 420 TRP cc_start: 0.7212 (m100) cc_final: 0.6583 (m100) REVERT: A 596 MET cc_start: 0.6827 (tpt) cc_final: 0.6566 (tpt) outliers start: 26 outliers final: 20 residues processed: 132 average time/residue: 0.1839 time to fit residues: 35.8839 Evaluate side-chains 137 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 331 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 600 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain A residue 182 GLU 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 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 654 LEU Chi-restraints excluded: chain A residue 699 LEU 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: 20.0000 chunk 102 optimal weight: 0.7980 chunk 105 optimal weight: 0.0980 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 92 optimal weight: 20.0000 chunk 67 optimal weight: 0.0070 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 503 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: 0.6094 moved from start: 0.1634 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= 0.160 Angle : 0.543 10.676 12771 Z= 0.271 Chirality : 0.038 0.211 1371 Planarity : 0.003 0.038 1605 Dihedral : 4.463 31.527 1292 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.86 % Allowed : 20.35 % Favored : 77.79 % 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: 1.54 (0.26), residues: 1148 helix: 1.63 (0.19), residues: 753 sheet: None (None), residues: 0 loop : -0.07 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 333 HIS 0.009 0.001 HIS A 378 PHE 0.029 0.001 PHE B 640 TYR 0.010 0.001 TYR B 462 ARG 0.004 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 139 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 0.985 Fit side-chains REVERT: B 197 MET cc_start: 0.5612 (tpt) cc_final: 0.5360 (mmm) REVERT: B 280 PHE cc_start: 0.7729 (t80) cc_final: 0.7487 (t80) REVERT: B 292 HIS cc_start: 0.7550 (OUTLIER) cc_final: 0.6579 (t-90) REVERT: B 382 MET cc_start: 0.4925 (ttt) cc_final: 0.3969 (ptt) REVERT: B 389 GLU cc_start: 0.7157 (tt0) cc_final: 0.6676 (tt0) REVERT: B 613 ILE cc_start: 0.8188 (mp) cc_final: 0.7809 (mt) REVERT: B 675 GLU cc_start: 0.7237 (pt0) cc_final: 0.6759 (tp30) REVERT: A 142 ARG cc_start: 0.6264 (ppt170) cc_final: 0.5711 (ppt170) REVERT: A 177 MET cc_start: 0.8184 (ttt) cc_final: 0.7983 (ttt) REVERT: A 206 MET cc_start: 0.6988 (tmm) cc_final: 0.6468 (tmm) REVERT: A 275 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7943 (mt) REVERT: A 382 MET cc_start: 0.5538 (ttm) cc_final: 0.4441 (ttm) REVERT: A 420 TRP cc_start: 0.7192 (m100) cc_final: 0.6555 (m100) REVERT: A 596 MET cc_start: 0.6673 (tpt) cc_final: 0.6441 (tpt) outliers start: 18 outliers final: 14 residues processed: 131 average time/residue: 0.1937 time to fit residues: 36.8664 Evaluate side-chains 133 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 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 368 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 699 LEU 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: 0.9980 chunk 75 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 0.2980 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 503 ASN ** 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: 0.6150 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9442 Z= 0.213 Angle : 0.584 10.664 12771 Z= 0.292 Chirality : 0.040 0.240 1371 Planarity : 0.003 0.040 1605 Dihedral : 4.459 32.111 1292 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.07 % Allowed : 20.45 % Favored : 77.48 % 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: 1.42 (0.26), residues: 1148 helix: 1.57 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -0.17 (0.35), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 300 HIS 0.012 0.001 HIS A 378 PHE 0.033 0.001 PHE B 640 TYR 0.012 0.001 TYR A 279 ARG 0.004 0.000 ARG B 473 ********************** 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 141 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 0.956 Fit side-chains REVERT: B 161 HIS cc_start: 0.7574 (t70) cc_final: 0.7308 (t70) REVERT: B 197 MET cc_start: 0.5591 (tpt) cc_final: 0.5303 (mmm) REVERT: B 292 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.6585 (t-90) REVERT: B 328 TYR cc_start: 0.4941 (m-80) cc_final: 0.4697 (m-80) REVERT: B 382 MET cc_start: 0.4860 (ttt) cc_final: 0.3879 (ptt) REVERT: B 389 GLU cc_start: 0.7219 (tt0) cc_final: 0.6730 (tt0) REVERT: A 142 ARG cc_start: 0.6243 (ppt170) cc_final: 0.5731 (ppt170) REVERT: A 275 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7926 (mt) REVERT: A 382 MET cc_start: 0.5440 (ttm) cc_final: 0.4369 (ttm) REVERT: A 420 TRP cc_start: 0.7195 (m100) cc_final: 0.6625 (m100) REVERT: A 596 MET cc_start: 0.6754 (tpt) cc_final: 0.6528 (tpt) outliers start: 20 outliers final: 16 residues processed: 134 average time/residue: 0.1816 time to fit residues: 35.9912 Evaluate side-chains 136 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 182 GLU 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 368 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 699 LEU 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: 0.8980 chunk 25 optimal weight: 0.3980 chunk 90 optimal weight: 9.9990 chunk 37 optimal weight: 0.0970 chunk 93 optimal weight: 30.0000 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 503 ASN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.267714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.199888 restraints weight = 9917.934| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.68 r_work: 0.3958 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.1708 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= 0.159 Angle : 0.554 10.705 12771 Z= 0.276 Chirality : 0.039 0.221 1371 Planarity : 0.003 0.037 1605 Dihedral : 4.306 30.040 1292 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.96 % Allowed : 20.35 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.26), residues: 1148 helix: 1.63 (0.19), residues: 753 sheet: None (None), residues: 0 loop : -0.05 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 333 HIS 0.010 0.001 HIS A 378 PHE 0.030 0.001 PHE B 640 TYR 0.009 0.001 TYR B 462 ARG 0.003 0.000 ARG B 473 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2168.73 seconds wall clock time: 39 minutes 13.12 seconds (2353.12 seconds total)