Starting phenix.real_space_refine on Fri Mar 15 01:43:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxk_35079/03_2024/8hxk_35079.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxk_35079/03_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_35079/03_2024/8hxk_35079.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxk_35079/03_2024/8hxk_35079.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxk_35079/03_2024/8hxk_35079.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxk_35079/03_2024/8hxk_35079.pdb" } 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 Residue "A GLU 37": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 512": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.83, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG 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: 4.22 Conformation dependent library (CDL) restraints added in 1.8 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: 0.94 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: 2.61 Time building geometry restraints manager: 4.53 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: 97.40 - 104.81: 190 104.81 - 112.21: 4955 112.21 - 119.61: 3894 119.61 - 127.02: 5258 127.02 - 134.42: 150 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 2.440 nonbonded pdb=" OH TYR B 203 " pdb=" OE2 GLU B 227 " model vdw 2.275 2.440 nonbonded pdb=" OE2 GLU B 294 " pdb=" OG SER B 312 " model vdw 2.277 2.440 nonbonded pdb=" NH2 ARG B 315 " pdb=" O PHE B 588 " model vdw 2.284 2.520 nonbonded pdb=" O VAL A 560 " pdb=" OG SER A 563 " model vdw 2.286 2.440 ... (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 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: 0.670 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: 0.000 Extract box with map and model: 3.700 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 29.050 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.840 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.146 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: 0.2300 time to fit residues: 71.9548 Evaluate side-chains 136 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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: 0.0050 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 98 optimal weight: 0.0970 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 73 optimal weight: 0.4980 chunk 114 optimal weight: 2.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5359 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10621 Z= 0.194 Angle : 0.707 8.899 14447 Z= 0.363 Chirality : 0.050 0.489 1573 Planarity : 0.006 0.108 1856 Dihedral : 6.963 57.263 1583 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 1.60 % Allowed : 9.96 % Favored : 88.44 % 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: -2.32 (0.22), residues: 1269 helix: -0.64 (0.26), residues: 404 sheet: -1.77 (0.51), residues: 84 loop : -2.10 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 461 HIS 0.011 0.002 HIS A 417 PHE 0.041 0.002 PHE A 512 TYR 0.017 0.002 TYR A 515 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 162 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 1.209 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 152 MET cc_start: 0.4587 (mmt) cc_final: 0.3968 (mmt) REVERT: A 180 TYR cc_start: 0.6634 (t80) cc_final: 0.6390 (t80) REVERT: A 270 MET cc_start: 0.3020 (tpt) cc_final: 0.2295 (tpt) REVERT: B 615 GLU cc_start: 0.7784 (mp0) cc_final: 0.7491 (mp0) outliers start: 18 outliers final: 14 residues processed: 158 average time/residue: 0.2259 time to fit residues: 50.6302 Evaluate side-chains 131 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 456 ASN 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: 10.0000 chunk 35 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 417 HIS A 508 ASN A 598 GLN A 599 ASN B 350 ASN B 436 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5694 moved from start: 0.3345 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= 0.216 Angle : 0.693 11.566 14447 Z= 0.355 Chirality : 0.050 0.484 1573 Planarity : 0.005 0.064 1856 Dihedral : 6.546 57.047 1583 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.31 % Allowed : 15.02 % Favored : 82.67 % 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: -2.21 (0.22), residues: 1269 helix: -0.41 (0.26), residues: 404 sheet: -1.69 (0.51), residues: 95 loop : -2.12 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 629 HIS 0.013 0.002 HIS B 34 PHE 0.025 0.002 PHE A 464 TYR 0.027 0.002 TYR A 199 ARG 0.010 0.001 ARG A 169 *********************** 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 156 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: A 152 MET cc_start: 0.4635 (mmt) cc_final: 0.3901 (mmt) REVERT: A 180 TYR cc_start: 0.6759 (t80) cc_final: 0.6432 (t80) REVERT: A 270 MET cc_start: 0.3722 (tpt) cc_final: 0.2854 (tpt) REVERT: B 398 VAL cc_start: 0.6898 (OUTLIER) cc_final: 0.6646 (m) REVERT: B 615 GLU cc_start: 0.7789 (mp0) cc_final: 0.7478 (mp0) outliers start: 26 outliers final: 18 residues processed: 151 average time/residue: 0.2263 time to fit residues: 48.5533 Evaluate side-chains 127 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 A residue 508 ASN Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 599 ASN 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 398 VAL Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 621 HIS 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: 20.0000 chunk 12 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 109 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- 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 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 10621 Z= 0.414 Angle : 0.890 14.434 14447 Z= 0.466 Chirality : 0.055 0.464 1573 Planarity : 0.007 0.088 1856 Dihedral : 7.032 56.849 1583 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 33.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.58 % Favored : 88.42 % Rotamer: Outliers : 4.09 % Allowed : 16.71 % Favored : 79.20 % 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: -2.65 (0.22), residues: 1269 helix: -0.77 (0.25), residues: 411 sheet: -2.44 (0.56), residues: 68 loop : -2.37 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP A 461 HIS 0.008 0.002 HIS A 417 PHE 0.028 0.003 PHE B 425 TYR 0.031 0.003 TYR A 510 ARG 0.018 0.001 ARG B 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 158 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 112 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.6667 (ppp) cc_final: 0.6437 (ppp) REVERT: A 508 ASN cc_start: 0.7529 (OUTLIER) cc_final: 0.7128 (p0) REVERT: A 596 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6290 (mp10) REVERT: B 325 PHE cc_start: 0.0933 (m-80) cc_final: 0.0670 (m-80) REVERT: B 540 ASN cc_start: 0.3855 (OUTLIER) cc_final: 0.1957 (t0) outliers start: 46 outliers final: 22 residues processed: 147 average time/residue: 0.1996 time to fit residues: 43.2780 Evaluate side-chains 117 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 596 GLN Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 674 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 508 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 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: 0.6491 moved from start: 0.6588 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= 0.220 Angle : 0.698 9.275 14447 Z= 0.358 Chirality : 0.050 0.437 1573 Planarity : 0.005 0.058 1856 Dihedral : 6.741 58.927 1583 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 2.31 % Allowed : 21.42 % 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: -2.51 (0.22), residues: 1269 helix: -0.52 (0.25), residues: 413 sheet: -2.39 (0.51), residues: 84 loop : -2.35 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 461 HIS 0.008 0.001 HIS B 34 PHE 0.022 0.002 PHE B 334 TYR 0.019 0.002 TYR A 50 ARG 0.005 0.001 ARG B 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 138 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8300 (tt) REVERT: A 455 MET cc_start: 0.6790 (ppp) cc_final: 0.6554 (ppp) REVERT: A 474 MET cc_start: 0.6326 (ppp) cc_final: 0.5460 (mtp) REVERT: B 132 ASN cc_start: 0.3958 (OUTLIER) cc_final: 0.3484 (m110) REVERT: B 243 ILE cc_start: 0.5716 (OUTLIER) cc_final: 0.5042 (pt) outliers start: 26 outliers final: 19 residues processed: 130 average time/residue: 0.2161 time to fit residues: 40.6920 Evaluate side-chains 118 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 274 PHE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 596 GLN 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 243 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 674 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 101 optimal weight: 0.0770 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 40.0000 overall best weight: 0.8144 ------------------------------------------------------------------------------- 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 524 GLN ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** 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: 0.6475 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10621 Z= 0.184 Angle : 0.698 13.569 14447 Z= 0.346 Chirality : 0.049 0.433 1573 Planarity : 0.005 0.060 1856 Dihedral : 6.409 55.500 1583 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.76 % Allowed : 22.31 % Favored : 74.93 % 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: -2.34 (0.22), residues: 1269 helix: -0.37 (0.25), residues: 411 sheet: -2.31 (0.52), residues: 84 loop : -2.24 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 461 HIS 0.008 0.001 HIS B 34 PHE 0.022 0.002 PHE B 338 TYR 0.028 0.001 TYR A 592 ARG 0.005 0.000 ARG A 245 *********************** 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 132 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8252 (tt) REVERT: A 210 GLU cc_start: 0.8021 (mp0) cc_final: 0.7801 (mp0) REVERT: A 421 MET cc_start: 0.6802 (ppp) cc_final: 0.6362 (ppp) REVERT: A 474 MET cc_start: 0.6198 (ppp) cc_final: 0.5726 (mtp) REVERT: A 552 LYS cc_start: 0.8474 (ptpt) cc_final: 0.7862 (ptpp) REVERT: B 22 ARG cc_start: 0.5012 (tpp80) cc_final: 0.3398 (tpt-90) REVERT: B 132 ASN cc_start: 0.3679 (OUTLIER) cc_final: 0.3236 (m110) outliers start: 31 outliers final: 22 residues processed: 125 average time/residue: 0.2041 time to fit residues: 37.5958 Evaluate side-chains 116 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 274 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 544 ILE 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 387 CYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 651 HIS 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: 3.9990 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 0.0000 chunk 48 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.7491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10621 Z= 0.214 Angle : 0.689 9.875 14447 Z= 0.348 Chirality : 0.049 0.440 1573 Planarity : 0.005 0.068 1856 Dihedral : 6.304 57.117 1583 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 3.11 % Allowed : 22.67 % Favored : 74.22 % 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: -0.41 (0.25), residues: 407 sheet: -2.37 (0.52), residues: 84 loop : -2.17 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 461 HIS 0.007 0.001 HIS A 34 PHE 0.031 0.002 PHE A 308 TYR 0.017 0.002 TYR A 50 ARG 0.009 0.001 ARG A 306 *********************** 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 143 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 108 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8318 (tt) REVERT: A 150 ASN cc_start: 0.8268 (p0) cc_final: 0.7971 (p0) REVERT: A 180 TYR cc_start: 0.7365 (t80) cc_final: 0.6889 (t80) REVERT: A 243 TYR cc_start: 0.7399 (t80) cc_final: 0.7129 (t80) REVERT: A 360 MET cc_start: 0.8049 (pmm) cc_final: 0.7547 (pmm) REVERT: B 132 ASN cc_start: 0.3675 (OUTLIER) cc_final: 0.3310 (m110) REVERT: B 293 SER cc_start: 0.7248 (OUTLIER) cc_final: 0.7032 (p) REVERT: B 325 PHE cc_start: 0.1284 (m-80) cc_final: 0.0466 (m-80) outliers start: 35 outliers final: 25 residues processed: 133 average time/residue: 0.1866 time to fit residues: 36.9688 Evaluate side-chains 125 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 274 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 544 ILE 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 132 ASN Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain B residue 675 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 77 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 116 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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 442 GLN ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.8815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10621 Z= 0.284 Angle : 0.794 17.250 14447 Z= 0.401 Chirality : 0.053 0.448 1573 Planarity : 0.006 0.048 1856 Dihedral : 6.679 59.204 1583 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 26.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 3.47 % Allowed : 22.67 % Favored : 73.87 % 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: -0.52 (0.25), residues: 401 sheet: -2.83 (0.49), residues: 83 loop : -2.12 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP A 328 HIS 0.010 0.002 HIS B 34 PHE 0.033 0.002 PHE A 308 TYR 0.023 0.002 TYR B 449 ARG 0.005 0.001 ARG A 306 *********************** 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 148 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 109 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7524 (mt) cc_final: 0.7241 (mt) REVERT: A 243 TYR cc_start: 0.8045 (t80) cc_final: 0.7420 (t80) REVERT: A 360 MET cc_start: 0.8193 (pmm) cc_final: 0.7695 (pmm) REVERT: A 552 LYS cc_start: 0.8615 (ptpt) cc_final: 0.8367 (ptpp) REVERT: B 132 ASN cc_start: 0.3986 (OUTLIER) cc_final: 0.3076 (m110) REVERT: B 325 PHE cc_start: 0.1786 (m-80) cc_final: 0.1575 (m-80) outliers start: 39 outliers final: 29 residues processed: 139 average time/residue: 0.2117 time to fit residues: 42.9475 Evaluate side-chains 132 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 544 ILE 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 237 PHE Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 621 HIS Chi-restraints excluded: chain B residue 651 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.4980 chunk 116 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 137 ASN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** 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: 0.6832 moved from start: 0.9118 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= 0.218 Angle : 0.746 10.851 14447 Z= 0.371 Chirality : 0.051 0.420 1573 Planarity : 0.005 0.046 1856 Dihedral : 6.391 58.127 1583 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.77 % Favored : 90.15 % Rotamer: Outliers : 2.40 % Allowed : 23.47 % Favored : 74.13 % 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: -0.47 (0.25), residues: 401 sheet: -2.63 (0.51), residues: 84 loop : -2.09 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 461 HIS 0.009 0.001 HIS B 34 PHE 0.037 0.002 PHE B 191 TYR 0.018 0.002 TYR A 50 ARG 0.004 0.001 ARG A 460 *********************** 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 129 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 TYR cc_start: 0.8031 (t80) cc_final: 0.7543 (t80) REVERT: A 434 THR cc_start: 0.8314 (m) cc_final: 0.8094 (p) REVERT: A 446 ILE cc_start: 0.8782 (tt) cc_final: 0.8223 (pt) REVERT: A 503 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7299 (mp) REVERT: B 387 CYS cc_start: 0.3621 (OUTLIER) cc_final: 0.2147 (m) outliers start: 27 outliers final: 21 residues processed: 122 average time/residue: 0.1971 time to fit residues: 35.0679 Evaluate side-chains 119 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 274 PHE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 544 ILE 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 364 LEU Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 466 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 125 optimal weight: 0.0000 chunk 115 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.9238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 10621 Z= 0.202 Angle : 0.740 12.743 14447 Z= 0.366 Chirality : 0.050 0.427 1573 Planarity : 0.005 0.073 1856 Dihedral : 6.228 57.968 1583 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.54 % Favored : 90.39 % Rotamer: Outliers : 1.96 % Allowed : 24.27 % Favored : 73.78 % 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: -2.20 (0.22), residues: 1269 helix: -0.40 (0.25), residues: 402 sheet: -2.47 (0.52), residues: 84 loop : -2.01 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 328 HIS 0.009 0.001 HIS B 34 PHE 0.028 0.002 PHE B 191 TYR 0.021 0.002 TYR A 592 ARG 0.006 0.001 ARG B 324 ********************** 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 127 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 TYR cc_start: 0.7622 (t80) cc_final: 0.7248 (t80) REVERT: A 243 TYR cc_start: 0.8056 (t80) cc_final: 0.7438 (t80) REVERT: A 446 ILE cc_start: 0.8714 (tt) cc_final: 0.8214 (pt) REVERT: A 503 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7342 (mp) REVERT: B 491 TYR cc_start: 0.7701 (m-80) cc_final: 0.7473 (m-10) outliers start: 22 outliers final: 20 residues processed: 121 average time/residue: 0.2131 time to fit residues: 37.9073 Evaluate side-chains 122 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 274 PHE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 544 ILE 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 364 LEU Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 466 THR 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: 0.9990 chunk 92 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 0.0050 chunk 18 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- 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 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN ** B 210 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 = 0.4502 r_free = 0.4502 target = 0.104869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.083613 restraints weight = 55329.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.086107 restraints weight = 31920.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.087772 restraints weight = 21475.969| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.9481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10621 Z= 0.200 Angle : 0.716 10.748 14447 Z= 0.357 Chirality : 0.049 0.429 1573 Planarity : 0.005 0.054 1856 Dihedral : 6.087 57.097 1583 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.85 % Favored : 90.07 % Rotamer: Outliers : 2.84 % Allowed : 23.73 % Favored : 73.42 % 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: -2.20 (0.22), residues: 1269 helix: -0.37 (0.25), residues: 401 sheet: -2.51 (0.51), residues: 84 loop : -2.02 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 461 HIS 0.009 0.001 HIS B 34 PHE 0.026 0.002 PHE B 191 TYR 0.017 0.002 TYR B 656 ARG 0.006 0.001 ARG A 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2218.40 seconds wall clock time: 41 minutes 3.85 seconds (2463.85 seconds total)