Starting phenix.real_space_refine on Fri Feb 14 17:24:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxk_35079/02_2025/8hxk_35079.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxk_35079/02_2025/8hxk_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/cci-nas-00/data/ceres_data/8hxk_35079/02_2025/8hxk_35079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxk_35079/02_2025/8hxk_35079.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxk_35079/02_2025/8hxk_35079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxk_35079/02_2025/8hxk_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-5592/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: 6.14, per 1000 atoms: 0.59 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: 2.60 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: 1.06 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: 3.29 Time building geometry restraints manager: 3.01 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.450 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.760 ------------------------------------------------------------------------------- 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 : 1.118 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: 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: 0.2418 time to fit residues: 75.8204 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 : 1.138 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.134679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.116328 restraints weight = 57360.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.119308 restraints weight = 33353.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.121147 restraints weight = 21676.181| |-----------------------------------------------------------------------------| r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5814 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 : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: A 152 MET cc_start: 0.4642 (mmt) cc_final: 0.3767 (mmt) REVERT: A 180 TYR cc_start: 0.7234 (t80) cc_final: 0.6940 (t80) REVERT: A 270 MET cc_start: 0.2811 (tpt) cc_final: 0.2172 (tpt) outliers start: 17 outliers final: 13 residues processed: 160 average time/residue: 0.2292 time to fit residues: 52.2251 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 : 1.197 ------------------------------------------------------------------------------- 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 66 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 112 optimal weight: 0.0000 chunk 123 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 B 350 ASN B 552 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.126226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.106337 restraints weight = 58930.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.109214 restraints weight = 33826.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.111038 restraints weight = 22081.565| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10621 Z= 0.257 Angle : 0.751 10.205 14447 Z= 0.391 Chirality : 0.052 0.503 1573 Planarity : 0.006 0.061 1856 Dihedral : 6.556 57.558 1583 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 2.04 % Allowed : 13.87 % Favored : 84.09 % 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: -2.35 (0.22), residues: 1269 helix: -0.66 (0.25), residues: 413 sheet: -1.91 (0.47), residues: 105 loop : -2.11 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 461 HIS 0.012 0.002 HIS A 417 PHE 0.029 0.002 PHE B 425 TYR 0.026 0.002 TYR A 237 ARG 0.013 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 156 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8523 (mp0) REVERT: A 152 MET cc_start: 0.4646 (mmt) cc_final: 0.3350 (mmt) REVERT: A 270 MET cc_start: 0.3440 (tpt) cc_final: 0.2738 (tpt) REVERT: B 398 VAL cc_start: 0.7032 (OUTLIER) cc_final: 0.6789 (m) outliers start: 23 outliers final: 13 residues processed: 149 average time/residue: 0.2262 time to fit residues: 48.3299 Evaluate side-chains 121 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 106 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 0.1980 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 609 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 = 0.4624 r_free = 0.4624 target = 0.119668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.097181 restraints weight = 53149.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.099931 restraints weight = 32454.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.101876 restraints weight = 22439.402| |-----------------------------------------------------------------------------| r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10621 Z= 0.255 Angle : 0.736 10.645 14447 Z= 0.377 Chirality : 0.051 0.468 1573 Planarity : 0.006 0.056 1856 Dihedral : 6.366 58.733 1583 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.38 % Favored : 90.54 % Rotamer: Outliers : 2.76 % Allowed : 16.80 % Favored : 80.44 % 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: -2.30 (0.22), residues: 1269 helix: -0.54 (0.25), residues: 412 sheet: -2.14 (0.52), residues: 80 loop : -2.11 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP A 461 HIS 0.010 0.002 HIS A 195 PHE 0.036 0.002 PHE A 72 TYR 0.029 0.002 TYR A 50 ARG 0.009 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 162 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TYR cc_start: -0.0339 (p90) cc_final: -0.0867 (p90) REVERT: A 180 TYR cc_start: 0.8043 (t80) cc_final: 0.7683 (t80) REVERT: A 455 MET cc_start: 0.6674 (ppp) cc_final: 0.6264 (ppp) REVERT: A 461 TRP cc_start: 0.8054 (m-90) cc_final: 0.7834 (m-90) REVERT: A 474 MET cc_start: 0.6121 (ppp) cc_final: 0.5141 (mmm) REVERT: A 596 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.6502 (mp10) REVERT: B 22 ARG cc_start: 0.4095 (tpp80) cc_final: 0.3366 (tpt-90) REVERT: B 132 ASN cc_start: 0.3534 (OUTLIER) cc_final: 0.3273 (m110) REVERT: B 491 TYR cc_start: 0.7465 (m-10) cc_final: 0.7195 (m-10) REVERT: B 615 GLU cc_start: 0.7696 (mp0) cc_final: 0.7477 (mp0) outliers start: 31 outliers final: 20 residues processed: 153 average time/residue: 0.2153 time to fit residues: 47.5325 Evaluate side-chains 133 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 333 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 456 LEU 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 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 127 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 298 THR 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 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 26 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 442 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** 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 = 0.4596 r_free = 0.4596 target = 0.117825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.096606 restraints weight = 59152.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.099313 restraints weight = 33589.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.100972 restraints weight = 22172.663| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10621 Z= 0.225 Angle : 0.699 13.553 14447 Z= 0.358 Chirality : 0.050 0.469 1573 Planarity : 0.005 0.056 1856 Dihedral : 6.233 57.621 1583 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 3.29 % Allowed : 17.33 % Favored : 79.38 % 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: -2.15 (0.23), residues: 1269 helix: -0.33 (0.25), residues: 413 sheet: -2.24 (0.47), residues: 103 loop : -2.02 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 461 HIS 0.010 0.002 HIS B 34 PHE 0.019 0.002 PHE B 338 TYR 0.016 0.002 TYR A 385 ARG 0.005 0.001 ARG A 518 *********************** 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 154 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 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: symmetry clash REVERT: A 95 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8537 (tt) REVERT: A 123 MET cc_start: 0.6719 (mmt) cc_final: 0.6162 (mmt) REVERT: A 270 MET cc_start: 0.3965 (tpt) cc_final: 0.3654 (tpt) REVERT: A 408 MET cc_start: 0.7139 (mmp) cc_final: 0.6760 (tmm) REVERT: A 461 TRP cc_start: 0.8150 (m-10) cc_final: 0.7836 (m-90) REVERT: A 468 ILE cc_start: 0.7206 (OUTLIER) cc_final: 0.6776 (mt) REVERT: A 474 MET cc_start: 0.5989 (ppp) cc_final: 0.5502 (mmm) REVERT: B 22 ARG cc_start: 0.4174 (tpp80) cc_final: 0.3598 (tpt-90) REVERT: B 132 ASN cc_start: 0.3043 (OUTLIER) cc_final: 0.2799 (m110) REVERT: B 491 TYR cc_start: 0.7705 (m-80) cc_final: 0.7444 (m-10) outliers start: 37 outliers final: 22 residues processed: 144 average time/residue: 0.2135 time to fit residues: 44.8967 Evaluate side-chains 136 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 295 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 456 LEU 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 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 256 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 476 CYS 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 111 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 122 optimal weight: 0.0170 chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.117244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.094955 restraints weight = 53210.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.097579 restraints weight = 32181.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.099444 restraints weight = 21859.504| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10621 Z= 0.177 Angle : 0.684 8.728 14447 Z= 0.344 Chirality : 0.049 0.453 1573 Planarity : 0.005 0.053 1856 Dihedral : 6.037 55.610 1583 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.76 % Allowed : 19.56 % Favored : 77.69 % 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: -0.25 (0.25), residues: 414 sheet: -2.13 (0.48), residues: 103 loop : -1.98 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 461 HIS 0.010 0.002 HIS A 195 PHE 0.018 0.002 PHE B 338 TYR 0.016 0.001 TYR A 385 ARG 0.004 0.000 ARG A 306 *********************** 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 149 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8377 (tt) REVERT: A 123 MET cc_start: 0.6798 (mmt) cc_final: 0.6200 (mmt) REVERT: A 180 TYR cc_start: 0.8188 (t80) cc_final: 0.7708 (t80) REVERT: A 270 MET cc_start: 0.3581 (tpt) cc_final: 0.3090 (tpt) REVERT: A 355 ASP cc_start: 0.6575 (t0) cc_final: 0.6284 (t0) REVERT: A 552 LYS cc_start: 0.7936 (ptpp) cc_final: 0.7590 (ptpp) REVERT: B 22 ARG cc_start: 0.4287 (tpp80) cc_final: 0.3707 (tpt-90) REVERT: B 132 ASN cc_start: 0.3429 (OUTLIER) cc_final: 0.3189 (m110) outliers start: 31 outliers final: 17 residues processed: 139 average time/residue: 0.2000 time to fit residues: 41.1076 Evaluate side-chains 128 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 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 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 430 ILE 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 44 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN ** B 559 GLN ** 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 = 0.4552 r_free = 0.4552 target = 0.114115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.091596 restraints weight = 54619.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.094361 restraints weight = 31984.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.096198 restraints weight = 21704.924| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.6671 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= 0.204 Angle : 0.712 17.969 14447 Z= 0.357 Chirality : 0.050 0.455 1573 Planarity : 0.005 0.062 1856 Dihedral : 5.939 55.767 1583 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 3.02 % Allowed : 20.36 % Favored : 76.62 % 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: -2.01 (0.23), residues: 1269 helix: -0.27 (0.25), residues: 413 sheet: -2.01 (0.49), residues: 103 loop : -1.92 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 461 HIS 0.009 0.001 HIS A 417 PHE 0.019 0.002 PHE B 338 TYR 0.022 0.002 TYR A 592 ARG 0.007 0.001 ARG A 115 *********************** 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 150 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8617 (tt) REVERT: A 270 MET cc_start: 0.3963 (tpt) cc_final: 0.3725 (tpt) REVERT: A 355 ASP cc_start: 0.6677 (t0) cc_final: 0.6297 (t0) REVERT: A 461 TRP cc_start: 0.8217 (m-10) cc_final: 0.7702 (m-10) REVERT: B 132 ASN cc_start: 0.3378 (OUTLIER) cc_final: 0.3145 (m110) REVERT: B 325 PHE cc_start: 0.2389 (m-80) cc_final: 0.1227 (m-80) outliers start: 34 outliers final: 19 residues processed: 140 average time/residue: 0.2038 time to fit residues: 42.2252 Evaluate side-chains 123 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 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 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 429 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 506 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 105 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 524 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 148 ASN B 210 ASN ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.105007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.083580 restraints weight = 54478.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.085573 restraints weight = 33873.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.088160 restraints weight = 22166.784| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.8698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 10621 Z= 0.354 Angle : 0.881 12.385 14447 Z= 0.454 Chirality : 0.055 0.487 1573 Planarity : 0.007 0.081 1856 Dihedral : 6.743 58.386 1583 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 26.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 2.84 % Allowed : 21.24 % 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: -2.27 (0.22), residues: 1269 helix: -0.56 (0.25), residues: 409 sheet: -2.56 (0.65), residues: 45 loop : -2.05 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 461 HIS 0.012 0.002 HIS A 34 PHE 0.030 0.003 PHE B 338 TYR 0.036 0.003 TYR B 449 ARG 0.010 0.001 ARG A 169 *********************** 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 to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8541 (tt) REVERT: A 176 LEU cc_start: 0.7834 (mt) cc_final: 0.7337 (mt) REVERT: A 468 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7419 (mt) REVERT: B 132 ASN cc_start: 0.3869 (OUTLIER) cc_final: 0.3438 (m110) REVERT: B 191 PHE cc_start: 0.0955 (OUTLIER) cc_final: 0.0731 (p90) REVERT: B 325 PHE cc_start: 0.3288 (m-80) cc_final: 0.2550 (m-80) REVERT: B 343 PHE cc_start: 0.7660 (m-10) cc_final: 0.7455 (m-80) outliers start: 32 outliers final: 24 residues processed: 142 average time/residue: 0.2295 time to fit residues: 46.5295 Evaluate side-chains 131 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 529 LEU 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 191 PHE 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 303 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 430 ILE 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 76 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 0.0870 chunk 72 optimal weight: 0.1980 chunk 58 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- 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 374 HIS ** 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 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.106072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.084413 restraints weight = 54847.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.087078 restraints weight = 31375.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.088713 restraints weight = 21065.285| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.8960 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= 0.217 Angle : 0.776 14.598 14447 Z= 0.390 Chirality : 0.051 0.428 1573 Planarity : 0.005 0.071 1856 Dihedral : 6.473 59.644 1583 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.14 % Favored : 90.78 % Rotamer: Outliers : 2.58 % Allowed : 22.40 % Favored : 75.02 % 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: -2.17 (0.22), residues: 1269 helix: -0.42 (0.25), residues: 408 sheet: -2.47 (0.61), residues: 51 loop : -2.03 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 461 HIS 0.007 0.001 HIS A 34 PHE 0.025 0.002 PHE B 338 TYR 0.033 0.002 TYR A 243 ARG 0.005 0.001 ARG B 563 *********************** 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 137 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8501 (tt) REVERT: A 176 LEU cc_start: 0.8002 (mt) cc_final: 0.7539 (mt) REVERT: A 270 MET cc_start: 0.4383 (tpp) cc_final: 0.4069 (tpp) REVERT: A 434 THR cc_start: 0.8541 (m) cc_final: 0.8327 (p) REVERT: A 468 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7330 (mt) REVERT: B 132 ASN cc_start: 0.3506 (OUTLIER) cc_final: 0.3091 (m-40) REVERT: B 325 PHE cc_start: 0.2874 (m-80) cc_final: 0.2165 (m-80) REVERT: B 511 PHE cc_start: 0.7783 (m-80) cc_final: 0.7489 (m-80) outliers start: 29 outliers final: 19 residues processed: 134 average time/residue: 0.2128 time to fit residues: 41.5541 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 : 1.086 ------------------------------------------------------------------------------- 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 333 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 468 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 270 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 506 VAL 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 38 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 148 ASN B 210 ASN ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.104747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.083340 restraints weight = 54719.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.085787 restraints weight = 31360.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.087413 restraints weight = 21092.808| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.9392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10621 Z= 0.237 Angle : 0.792 12.781 14447 Z= 0.401 Chirality : 0.052 0.437 1573 Planarity : 0.006 0.086 1856 Dihedral : 6.308 57.014 1583 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.56 % Favored : 89.36 % Rotamer: Outliers : 2.40 % Allowed : 22.93 % Favored : 74.67 % 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: -2.19 (0.22), residues: 1269 helix: -0.42 (0.25), residues: 404 sheet: -2.39 (0.62), residues: 51 loop : -2.05 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 461 HIS 0.006 0.001 HIS A 34 PHE 0.027 0.002 PHE B 191 TYR 0.032 0.002 TYR A 243 ARG 0.008 0.001 ARG B 194 ********************** 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 133 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8546 (tt) REVERT: A 150 ASN cc_start: 0.8820 (p0) cc_final: 0.8381 (p0) REVERT: A 176 LEU cc_start: 0.8199 (mt) cc_final: 0.7728 (mt) REVERT: A 360 MET cc_start: 0.8442 (pmm) cc_final: 0.7986 (pmm) REVERT: A 434 THR cc_start: 0.8620 (m) cc_final: 0.8415 (p) REVERT: A 468 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7445 (mt) REVERT: B 132 ASN cc_start: 0.3586 (OUTLIER) cc_final: 0.3246 (m-40) outliers start: 27 outliers final: 20 residues processed: 131 average time/residue: 0.2064 time to fit residues: 39.7104 Evaluate side-chains 124 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 333 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 468 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 270 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 59 optimal weight: 30.0000 chunk 37 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 508 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.103357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.081824 restraints weight = 54546.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.084375 restraints weight = 31115.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.085983 restraints weight = 20923.534| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.9878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10621 Z= 0.239 Angle : 0.801 12.484 14447 Z= 0.406 Chirality : 0.051 0.427 1573 Planarity : 0.006 0.060 1856 Dihedral : 6.197 56.223 1583 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 2.04 % Allowed : 23.82 % 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: -2.21 (0.22), residues: 1269 helix: -0.47 (0.25), residues: 396 sheet: -2.27 (0.62), residues: 51 loop : -2.04 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 271 HIS 0.007 0.001 HIS A 34 PHE 0.029 0.002 PHE B 191 TYR 0.024 0.002 TYR A 592 ARG 0.016 0.001 ARG A 245 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3922.63 seconds wall clock time: 71 minutes 0.32 seconds (4260.32 seconds total)