Starting phenix.real_space_refine on Sat Nov 16 05:46:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxk_35079/11_2024/8hxk_35079.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxk_35079/11_2024/8hxk_35079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxk_35079/11_2024/8hxk_35079.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxk_35079/11_2024/8hxk_35079.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxk_35079/11_2024/8hxk_35079.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxk_35079/11_2024/8hxk_35079.cif" } resolution = 3.8 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= 0.002 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 54 5.16 5 C 6596 2.51 5 N 1709 2.21 5 O 1981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10340 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4894 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 566} Chain: "B" Number of atoms: 5320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5320 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 34, 'TRANS': 641} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.21, per 1000 atoms: 0.60 Number of scatterers: 10340 At special positions: 0 Unit cell: (81.62, 107.06, 156.88, 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 54 16.00 O 1981 8.00 N 1709 7.00 C 6596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 357 " distance=2.02 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 428 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 521 " distance=2.04 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 484 " distance=2.02 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 586 " distance=2.04 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 667 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 701 " - " ASN A 322 " " NAG A 702 " - " ASN A 432 " " NAG A 703 " - " ASN A 546 " " NAG A 704 " - " ASN A 329 " " NAG B1301 " - " ASN B 366 " " NAG C 1 " - " ASN A 53 " " NAG D 1 " - " ASN B 339 " Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.2 seconds 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 33.2% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.715A pdb=" N ARG A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 79 removed outlier: 4.244A pdb=" N GLN A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 109 through 128 Processing helix chain 'A' and resid 158 through 193 removed outlier: 5.429A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.650A pdb=" N ALA A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 232 removed outlier: 4.194A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 4.255A pdb=" N ASP A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.548A pdb=" N ARG A 273 " --> pdb=" O MET A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 399 through 413 removed outlier: 4.298A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 448 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 481 removed outlier: 3.631A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 removed outlier: 4.084A pdb=" N SER A 502 " --> pdb=" O ASP A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.994A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 561 removed outlier: 4.121A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 Processing helix chain 'A' and resid 581 through 597 removed outlier: 3.592A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Proline residue: A 590 - end of helix Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 399 through 406 Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 627 through 632 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 removed outlier: 3.822A pdb=" N VAL A 132 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE A 142 " --> pdb=" O VAL A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.486A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 31 removed outlier: 8.188A pdb=" N ASN B 62 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR B 265 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR B 203 " --> pdb=" O VAL B 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 56 removed outlier: 3.836A pdb=" N VAL B 285 " --> pdb=" O MET B 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.984A pdb=" N LEU B 84 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AA8, first strand: chain 'B' and resid 195 through 196 Processing sheet with id=AA9, first strand: chain 'B' and resid 321 through 323 removed outlier: 8.156A pdb=" N ILE B 322 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 579 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 357 through 358 removed outlier: 6.828A pdb=" N CYS B 357 " --> pdb=" O CYS B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 390 through 392 Processing sheet with id=AB3, first strand: chain 'B' and resid 395 through 398 Processing sheet with id=AB4, first strand: chain 'B' and resid 448 through 450 Processing sheet with id=AB5, first strand: chain 'B' and resid 607 through 609 removed outlier: 6.687A pdb=" N CYS B 645 " --> pdb=" O TYR B 608 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 951 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: 2.97 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3263 1.34 - 1.46: 2704 1.46 - 1.59: 4574 1.59 - 1.71: 0 1.71 - 1.83: 80 Bond restraints: 10621 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.21e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.18e+00 bond pdb=" CB ASP B 85 " pdb=" CG ASP B 85 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.45e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.20e+00 ... (remaining 10616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 14156 2.98 - 5.96: 235 5.96 - 8.94: 44 8.94 - 11.92: 9 11.92 - 14.90: 3 Bond angle restraints: 14447 Sorted by residual: angle pdb=" O GLY A 66 " pdb=" C GLY A 66 " pdb=" N ALA A 67 " ideal model delta sigma weight residual 121.85 124.86 -3.01 5.60e-01 3.19e+00 2.88e+01 angle pdb=" N GLY A 66 " pdb=" CA GLY A 66 " pdb=" C GLY A 66 " ideal model delta sigma weight residual 110.21 105.50 4.71 9.10e-01 1.21e+00 2.68e+01 angle pdb=" CB MET A 557 " pdb=" CG MET A 557 " pdb=" SD MET A 557 " ideal model delta sigma weight residual 112.70 127.30 -14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" CA LEU A 450 " pdb=" CB LEU A 450 " pdb=" CG LEU A 450 " ideal model delta sigma weight residual 116.30 131.20 -14.90 3.50e+00 8.16e-02 1.81e+01 angle pdb=" N GLN A 556 " pdb=" CA GLN A 556 " pdb=" CB GLN A 556 " ideal model delta sigma weight residual 110.28 116.78 -6.50 1.55e+00 4.16e-01 1.76e+01 ... (remaining 14442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5683 17.74 - 35.48: 571 35.48 - 53.22: 119 53.22 - 70.96: 13 70.96 - 88.71: 12 Dihedral angle restraints: 6398 sinusoidal: 2670 harmonic: 3728 Sorted by residual: dihedral pdb=" CB CYS B 534 " pdb=" SG CYS B 534 " pdb=" SG CYS B 586 " pdb=" CB CYS B 586 " ideal model delta sinusoidal sigma weight residual -86.00 -5.22 -80.78 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CA CYS B 387 " pdb=" C CYS B 387 " pdb=" N PHE B 388 " pdb=" CA PHE B 388 " ideal model delta harmonic sigma weight residual -180.00 -143.91 -36.09 0 5.00e+00 4.00e-02 5.21e+01 dihedral pdb=" CB CYS B 658 " pdb=" SG CYS B 658 " pdb=" SG CYS B 667 " pdb=" CB CYS B 667 " ideal model delta sinusoidal sigma weight residual -86.00 -135.08 49.08 1 1.00e+01 1.00e-02 3.31e+01 ... (remaining 6395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1485 0.117 - 0.234: 80 0.234 - 0.351: 7 0.351 - 0.468: 0 0.468 - 0.585: 1 Chirality restraints: 1573 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 53 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.55e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 339 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 366 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 1570 not shown) Planarity restraints: 1863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 444 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.21e+00 pdb=" C LEU A 444 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU A 444 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN A 445 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 388 " 0.017 2.00e-02 2.50e+03 1.94e-02 6.59e+00 pdb=" CG PHE B 388 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE B 388 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 388 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 388 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 388 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 388 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 582 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO A 583 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.034 5.00e-02 4.00e+02 ... (remaining 1860 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 429 2.71 - 3.26: 10927 3.26 - 3.80: 18841 3.80 - 4.35: 23214 4.35 - 4.90: 36815 Nonbonded interactions: 90226 Sorted by model distance: nonbonded pdb=" O ASP B 286 " pdb=" OG SER B 293 " model vdw 2.159 3.040 nonbonded pdb=" OH TYR B 203 " pdb=" OE2 GLU B 227 " model vdw 2.275 3.040 nonbonded pdb=" OE2 GLU B 294 " pdb=" OG SER B 312 " model vdw 2.277 3.040 nonbonded pdb=" NH2 ARG B 315 " pdb=" O PHE B 588 " model vdw 2.284 3.120 nonbonded pdb=" O VAL A 560 " pdb=" OG SER A 563 " model vdw 2.286 3.040 ... (remaining 90221 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.800 Find NCS groups from input model: 0.190 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5073 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 0.083 10621 Z= 0.319 Angle : 0.996 14.902 14447 Z= 0.512 Chirality : 0.062 0.585 1573 Planarity : 0.007 0.061 1856 Dihedral : 14.606 88.705 3973 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.65 (0.21), residues: 1269 helix: -1.15 (0.24), residues: 400 sheet: -1.87 (0.54), residues: 74 loop : -2.18 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 610 HIS 0.016 0.002 HIS A 34 PHE 0.044 0.003 PHE B 388 TYR 0.029 0.003 TYR B 67 ARG 0.008 0.001 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.7883 (pp20) cc_final: 0.7475 (pp20) REVERT: A 34 HIS cc_start: 0.5397 (m90) cc_final: 0.4890 (m90) REVERT: A 179 LEU cc_start: 0.7561 (tt) cc_final: 0.7210 (mp) REVERT: A 180 TYR cc_start: 0.6582 (t80) cc_final: 0.6255 (t80) REVERT: A 270 MET cc_start: 0.2534 (tpt) cc_final: 0.2294 (tpt) REVERT: B 615 GLU cc_start: 0.7785 (mp0) cc_final: 0.7478 (mp0) REVERT: B 656 TYR cc_start: 0.6479 (t80) cc_final: 0.6276 (t80) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2384 time to fit residues: 74.7547 Evaluate side-chains 136 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9980 chunk 95 optimal weight: 0.0020 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 98 optimal weight: 0.0370 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 73 optimal weight: 0.2980 chunk 114 optimal weight: 4.9990 overall best weight: 0.3866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5342 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10621 Z= 0.225 Angle : 0.737 9.196 14447 Z= 0.380 Chirality : 0.051 0.500 1573 Planarity : 0.006 0.093 1856 Dihedral : 6.980 56.544 1583 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 1.51 % Allowed : 9.69 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.38 (0.22), residues: 1269 helix: -0.73 (0.25), residues: 411 sheet: -1.96 (0.47), residues: 103 loop : -2.09 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 461 HIS 0.012 0.002 HIS A 505 PHE 0.042 0.003 PHE A 512 TYR 0.021 0.002 TYR A 237 ARG 0.007 0.001 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: A 152 MET cc_start: 0.4624 (mmt) cc_final: 0.3720 (mmt) REVERT: A 180 TYR cc_start: 0.6643 (t80) cc_final: 0.6408 (t80) REVERT: A 270 MET cc_start: 0.3025 (tpt) cc_final: 0.2246 (tpt) REVERT: B 615 GLU cc_start: 0.7748 (mp0) cc_final: 0.7475 (mp0) outliers start: 17 outliers final: 13 residues processed: 160 average time/residue: 0.2349 time to fit residues: 53.9717 Evaluate side-chains 132 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 674 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN B 350 ASN B 552 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5823 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10621 Z= 0.269 Angle : 0.746 10.289 14447 Z= 0.387 Chirality : 0.052 0.506 1573 Planarity : 0.006 0.062 1856 Dihedral : 6.576 57.549 1583 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 1.87 % Allowed : 13.87 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.39 (0.22), residues: 1269 helix: -0.69 (0.25), residues: 413 sheet: -1.95 (0.52), residues: 87 loop : -2.14 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP A 461 HIS 0.012 0.002 HIS A 417 PHE 0.024 0.002 PHE A 512 TYR 0.026 0.002 TYR A 199 ARG 0.010 0.001 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.4730 (mmt) cc_final: 0.3397 (mmt) REVERT: A 270 MET cc_start: 0.3698 (tpt) cc_final: 0.2683 (tpt) REVERT: B 398 VAL cc_start: 0.7066 (OUTLIER) cc_final: 0.6835 (m) outliers start: 21 outliers final: 14 residues processed: 147 average time/residue: 0.2229 time to fit residues: 47.4800 Evaluate side-chains 120 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 674 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 30.0000 chunk 12 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 109 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10621 Z= 0.247 Angle : 0.719 10.957 14447 Z= 0.373 Chirality : 0.051 0.481 1573 Planarity : 0.006 0.059 1856 Dihedral : 6.419 59.178 1583 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.76 % Allowed : 16.98 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.32 (0.22), residues: 1269 helix: -0.56 (0.25), residues: 412 sheet: -2.07 (0.53), residues: 80 loop : -2.13 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 461 HIS 0.029 0.002 HIS A 417 PHE 0.036 0.002 PHE A 72 TYR 0.031 0.002 TYR A 50 ARG 0.007 0.001 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7079 (mt) cc_final: 0.6539 (mt) REVERT: A 408 MET cc_start: 0.6598 (tmm) cc_final: 0.6108 (tmm) REVERT: A 455 MET cc_start: 0.5920 (ppp) cc_final: 0.4745 (ppp) REVERT: A 468 ILE cc_start: 0.6910 (OUTLIER) cc_final: 0.6258 (mt) REVERT: B 22 ARG cc_start: 0.4386 (tpp80) cc_final: 0.3188 (tpt-90) REVERT: B 398 VAL cc_start: 0.7284 (OUTLIER) cc_final: 0.7048 (m) REVERT: B 433 ASN cc_start: 0.8447 (t0) cc_final: 0.8129 (t0) outliers start: 31 outliers final: 18 residues processed: 156 average time/residue: 0.2259 time to fit residues: 50.7038 Evaluate side-chains 132 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 556 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10621 Z= 0.223 Angle : 0.699 8.694 14447 Z= 0.364 Chirality : 0.050 0.476 1573 Planarity : 0.005 0.058 1856 Dihedral : 6.232 58.087 1583 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 2.67 % Allowed : 18.58 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.14 (0.23), residues: 1269 helix: -0.38 (0.26), residues: 412 sheet: -1.89 (0.49), residues: 103 loop : -2.04 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP A 461 HIS 0.012 0.002 HIS B 34 PHE 0.019 0.002 PHE B 338 TYR 0.017 0.002 TYR A 50 ARG 0.006 0.001 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7265 (mt) cc_final: 0.6732 (mt) REVERT: A 270 MET cc_start: 0.4069 (tpt) cc_final: 0.3292 (tpt) REVERT: B 22 ARG cc_start: 0.4604 (tpp80) cc_final: 0.3412 (tpt-90) REVERT: B 132 ASN cc_start: 0.3440 (OUTLIER) cc_final: 0.2977 (m110) REVERT: B 293 SER cc_start: 0.7115 (OUTLIER) cc_final: 0.6815 (p) outliers start: 30 outliers final: 18 residues processed: 147 average time/residue: 0.2226 time to fit residues: 46.6641 Evaluate side-chains 127 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 534 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 24 optimal weight: 0.0030 chunk 71 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 210 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10621 Z= 0.188 Angle : 0.675 8.187 14447 Z= 0.346 Chirality : 0.049 0.453 1573 Planarity : 0.005 0.056 1856 Dihedral : 6.042 56.467 1583 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.76 % Allowed : 19.73 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.18 (0.22), residues: 1269 helix: -0.46 (0.25), residues: 420 sheet: -1.92 (0.50), residues: 98 loop : -2.04 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 461 HIS 0.010 0.002 HIS A 195 PHE 0.019 0.002 PHE B 338 TYR 0.020 0.002 TYR A 50 ARG 0.005 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8154 (tt) REVERT: A 176 LEU cc_start: 0.7408 (mt) cc_final: 0.6857 (mt) REVERT: A 297 MET cc_start: 0.7431 (mmp) cc_final: 0.7222 (mmt) REVERT: A 462 MET cc_start: 0.6461 (tpp) cc_final: 0.5971 (mmm) REVERT: B 132 ASN cc_start: 0.3545 (OUTLIER) cc_final: 0.3097 (m110) REVERT: B 293 SER cc_start: 0.7109 (OUTLIER) cc_final: 0.6804 (p) outliers start: 31 outliers final: 17 residues processed: 135 average time/residue: 0.2221 time to fit residues: 43.6885 Evaluate side-chains 121 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 534 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 0.1980 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 76 optimal weight: 0.5980 chunk 74 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.6476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10621 Z= 0.180 Angle : 0.686 11.202 14447 Z= 0.347 Chirality : 0.050 0.450 1573 Planarity : 0.005 0.056 1856 Dihedral : 5.915 54.872 1583 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.67 % Allowed : 21.24 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.16 (0.22), residues: 1269 helix: -0.48 (0.25), residues: 421 sheet: -1.90 (0.51), residues: 98 loop : -2.00 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 461 HIS 0.005 0.001 HIS A 34 PHE 0.021 0.002 PHE B 338 TYR 0.018 0.001 TYR A 237 ARG 0.005 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8072 (tt) REVERT: A 176 LEU cc_start: 0.7328 (mt) cc_final: 0.6857 (mt) REVERT: A 270 MET cc_start: 0.3565 (tpt) cc_final: 0.2707 (tpp) REVERT: A 297 MET cc_start: 0.7250 (mmp) cc_final: 0.6972 (mmt) REVERT: B 22 ARG cc_start: 0.4435 (tpt170) cc_final: 0.4093 (mmm160) REVERT: B 132 ASN cc_start: 0.3536 (OUTLIER) cc_final: 0.3079 (m110) REVERT: B 325 PHE cc_start: 0.0153 (m-80) cc_final: -0.0482 (m-80) outliers start: 30 outliers final: 20 residues processed: 133 average time/residue: 0.2110 time to fit residues: 41.5570 Evaluate side-chains 124 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 674 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 0.0570 chunk 77 optimal weight: 10.0000 chunk 82 optimal weight: 0.0570 chunk 60 optimal weight: 6.9990 chunk 11 optimal weight: 0.0970 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 overall best weight: 0.8418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10621 Z= 0.178 Angle : 0.697 14.061 14447 Z= 0.351 Chirality : 0.049 0.448 1573 Planarity : 0.005 0.055 1856 Dihedral : 5.802 54.133 1583 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 2.40 % Allowed : 21.69 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.07 (0.23), residues: 1269 helix: -0.38 (0.25), residues: 416 sheet: -1.93 (0.50), residues: 98 loop : -1.95 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 461 HIS 0.006 0.001 HIS A 417 PHE 0.017 0.002 PHE B 388 TYR 0.018 0.001 TYR A 237 ARG 0.006 0.000 ARG B 563 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7980 (mtm180) cc_final: 0.7716 (mtt-85) REVERT: A 95 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8102 (tt) REVERT: A 176 LEU cc_start: 0.7159 (mt) cc_final: 0.6772 (mt) REVERT: A 297 MET cc_start: 0.7266 (mmp) cc_final: 0.7006 (mmt) REVERT: A 408 MET cc_start: 0.7141 (mmp) cc_final: 0.6909 (tmm) REVERT: A 474 MET cc_start: 0.6045 (ppp) cc_final: 0.5617 (ttm) REVERT: B 132 ASN cc_start: 0.3553 (OUTLIER) cc_final: 0.2695 (m-40) REVERT: B 262 TYR cc_start: 0.3244 (m-10) cc_final: 0.2906 (m-10) REVERT: B 325 PHE cc_start: 0.0241 (m-80) cc_final: -0.0314 (m-80) outliers start: 27 outliers final: 20 residues processed: 130 average time/residue: 0.2299 time to fit residues: 43.7410 Evaluate side-chains 126 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 534 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.7136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10621 Z= 0.195 Angle : 0.720 11.438 14447 Z= 0.365 Chirality : 0.050 0.450 1573 Planarity : 0.005 0.055 1856 Dihedral : 5.764 54.477 1583 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.90 % Favored : 91.02 % Rotamer: Outliers : 2.40 % Allowed : 21.16 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.98 (0.23), residues: 1269 helix: -0.36 (0.25), residues: 411 sheet: -2.17 (0.52), residues: 90 loop : -1.81 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 461 HIS 0.013 0.001 HIS B 34 PHE 0.034 0.002 PHE B 92 TYR 0.017 0.001 TYR A 237 ARG 0.005 0.000 ARG B 245 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8023 (mtm180) cc_final: 0.7745 (mtt-85) REVERT: A 95 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8182 (tt) REVERT: A 176 LEU cc_start: 0.7416 (mt) cc_final: 0.7018 (mt) REVERT: A 297 MET cc_start: 0.7357 (mmp) cc_final: 0.7101 (mmt) REVERT: A 408 MET cc_start: 0.7112 (mmp) cc_final: 0.6863 (tmm) REVERT: A 474 MET cc_start: 0.5934 (ppp) cc_final: 0.5689 (mtp) REVERT: B 129 LYS cc_start: 0.4364 (OUTLIER) cc_final: 0.3994 (mtmm) REVERT: B 132 ASN cc_start: 0.3697 (OUTLIER) cc_final: 0.2855 (m-40) REVERT: B 325 PHE cc_start: 0.0380 (m-80) cc_final: -0.0033 (m-80) outliers start: 27 outliers final: 19 residues processed: 125 average time/residue: 0.2210 time to fit residues: 40.0547 Evaluate side-chains 125 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 534 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 99 optimal weight: 0.0020 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 210 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.7416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10621 Z= 0.186 Angle : 0.744 16.159 14447 Z= 0.371 Chirality : 0.050 0.442 1573 Planarity : 0.005 0.054 1856 Dihedral : 5.778 54.421 1583 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.43 % Favored : 91.49 % Rotamer: Outliers : 2.13 % Allowed : 21.60 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.94 (0.23), residues: 1269 helix: -0.37 (0.25), residues: 411 sheet: -1.98 (0.58), residues: 74 loop : -1.80 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 461 HIS 0.010 0.001 HIS B 34 PHE 0.033 0.002 PHE B 92 TYR 0.017 0.001 TYR A 385 ARG 0.006 0.000 ARG B 563 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8013 (mtm180) cc_final: 0.7562 (mtp85) REVERT: A 95 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8199 (tt) REVERT: A 176 LEU cc_start: 0.7335 (mt) cc_final: 0.6995 (mt) REVERT: A 180 TYR cc_start: 0.7316 (t80) cc_final: 0.6747 (t80) REVERT: A 248 LEU cc_start: 0.9166 (mp) cc_final: 0.8900 (mp) REVERT: A 297 MET cc_start: 0.7571 (mmp) cc_final: 0.7297 (mmt) REVERT: B 22 ARG cc_start: 0.4419 (tpt170) cc_final: 0.3855 (mmm160) REVERT: B 129 LYS cc_start: 0.4288 (OUTLIER) cc_final: 0.3980 (mtmm) REVERT: B 132 ASN cc_start: 0.3426 (OUTLIER) cc_final: 0.2516 (m-40) REVERT: B 513 LEU cc_start: 0.6541 (tp) cc_final: 0.6298 (tp) outliers start: 24 outliers final: 18 residues processed: 131 average time/residue: 0.2253 time to fit residues: 43.3172 Evaluate side-chains 128 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 534 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 14 optimal weight: 0.0870 chunk 27 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN B 210 ASN ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.112395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.090304 restraints weight = 54555.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.093043 restraints weight = 31576.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.094780 restraints weight = 21149.359| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.7714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 10621 Z= 0.194 Angle : 0.739 14.261 14447 Z= 0.372 Chirality : 0.050 0.443 1573 Planarity : 0.005 0.046 1856 Dihedral : 5.721 54.877 1583 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 1.96 % Allowed : 22.04 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.91 (0.23), residues: 1269 helix: -0.35 (0.25), residues: 410 sheet: -1.97 (0.57), residues: 74 loop : -1.77 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 461 HIS 0.008 0.001 HIS B 34 PHE 0.028 0.002 PHE B 191 TYR 0.017 0.001 TYR A 237 ARG 0.006 0.000 ARG B 563 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2325.59 seconds wall clock time: 43 minutes 40.32 seconds (2620.32 seconds total)