Starting phenix.real_space_refine on Mon Jun 9 08:50:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxk_35079/06_2025/8hxk_35079.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxk_35079/06_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_35079/06_2025/8hxk_35079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxk_35079/06_2025/8hxk_35079.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxk_35079/06_2025/8hxk_35079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxk_35079/06_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-5710/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: 6.64, per 1000 atoms: 0.64 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: 3.16 Conformation dependent library (CDL) restraints added in 1.3 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: 1.25 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: 3.27 Time building geometry restraints manager: 3.46 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 27.780 Find NCS groups from input model: 0.210 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.250 ------------------------------------------------------------------------------- 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 10643 Z= 0.233 Angle : 1.035 21.385 14500 Z= 0.520 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01037 ( 7) link_NAG-ASN : angle 5.20518 ( 21) link_BETA1-4 : bond 0.04199 ( 2) link_BETA1-4 : angle 9.95397 ( 6) hydrogen bonds : bond 0.12739 ( 336) hydrogen bonds : angle 7.43939 ( 951) SS BOND : bond 0.00588 ( 13) SS BOND : angle 1.49857 ( 26) covalent geometry : bond 0.00492 (10621) covalent geometry : angle 0.99558 (14447) *********************** 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 : 1.309 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: 0.2390 time to fit residues: 75.2944 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 : 1.095 ------------------------------------------------------------------------------- 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: 0.0980 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: 0.0020 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: 0.3988 ------------------------------------------------------------------------------- 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 = 0.4819 r_free = 0.4819 target = 0.134570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.116096 restraints weight = 57790.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.119083 restraints weight = 33641.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.120925 restraints weight = 21907.704| |-----------------------------------------------------------------------------| r_work (final): 0.4544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5824 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10643 Z= 0.154 Angle : 0.774 16.477 14500 Z= 0.387 Chirality : 0.051 0.507 1573 Planarity : 0.006 0.097 1856 Dihedral : 6.928 58.145 1583 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 1.60 % Allowed : 9.60 % 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: -2.39 (0.22), residues: 1269 helix: -0.74 (0.25), residues: 411 sheet: -1.99 (0.47), residues: 103 loop : -2.09 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 461 HIS 0.012 0.002 HIS A 505 PHE 0.045 0.003 PHE A 512 TYR 0.017 0.002 TYR B 491 ARG 0.008 0.001 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00833 ( 7) link_NAG-ASN : angle 4.42308 ( 21) link_BETA1-4 : bond 0.02349 ( 2) link_BETA1-4 : angle 7.47043 ( 6) hydrogen bonds : bond 0.04799 ( 336) hydrogen bonds : angle 6.20666 ( 951) SS BOND : bond 0.00332 ( 13) SS BOND : angle 1.68869 ( 26) covalent geometry : bond 0.00330 (10621) covalent geometry : angle 0.73743 (14447) *********************** 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 166 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 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 37 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8358 (mp0) REVERT: A 152 MET cc_start: 0.4495 (mmt) cc_final: 0.3648 (mmt) REVERT: A 180 TYR cc_start: 0.7223 (t80) cc_final: 0.6963 (t80) REVERT: A 270 MET cc_start: 0.2710 (tpt) cc_final: 0.2177 (tpt) REVERT: B 469 TYR cc_start: 0.7933 (t80) cc_final: 0.7720 (t80) outliers start: 18 outliers final: 14 residues processed: 161 average time/residue: 0.2277 time to fit residues: 52.4974 Evaluate side-chains 133 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 474 MET 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: 2.9990 chunk 11 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 109 optimal weight: 0.0010 chunk 88 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 123 optimal weight: 0.1980 overall best weight: 0.8392 ------------------------------------------------------------------------------- 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 A 417 HIS ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.131170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.112148 restraints weight = 59328.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.115108 restraints weight = 34473.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.116947 restraints weight = 22448.063| |-----------------------------------------------------------------------------| r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10643 Z= 0.145 Angle : 0.740 15.770 14500 Z= 0.370 Chirality : 0.050 0.496 1573 Planarity : 0.005 0.062 1856 Dihedral : 6.507 58.009 1583 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 1.87 % Allowed : 14.22 % Favored : 83.91 % 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: -2.30 (0.22), residues: 1269 helix: -0.63 (0.25), residues: 413 sheet: -1.88 (0.48), residues: 103 loop : -2.08 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 461 HIS 0.012 0.002 HIS B 34 PHE 0.024 0.002 PHE A 512 TYR 0.022 0.002 TYR A 237 ARG 0.009 0.001 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00791 ( 7) link_NAG-ASN : angle 4.30234 ( 21) link_BETA1-4 : bond 0.02920 ( 2) link_BETA1-4 : angle 7.36099 ( 6) hydrogen bonds : bond 0.04609 ( 336) hydrogen bonds : angle 6.01894 ( 951) SS BOND : bond 0.00269 ( 13) SS BOND : angle 1.28675 ( 26) covalent geometry : bond 0.00305 (10621) covalent geometry : angle 0.70463 (14447) *********************** 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 150 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8470 (mp0) REVERT: A 152 MET cc_start: 0.4544 (mmt) cc_final: 0.3434 (mmt) REVERT: A 180 TYR cc_start: 0.7387 (t80) cc_final: 0.7001 (t80) REVERT: A 270 MET cc_start: 0.3440 (tpt) cc_final: 0.2912 (tpt) REVERT: A 408 MET cc_start: 0.6260 (tmm) cc_final: 0.5727 (tmm) REVERT: A 421 MET cc_start: 0.6508 (ppp) cc_final: 0.6198 (ppp) REVERT: A 455 MET cc_start: 0.5231 (ppp) cc_final: 0.5022 (ppp) REVERT: A 459 TRP cc_start: 0.7053 (t60) cc_final: 0.6744 (t60) REVERT: A 591 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6980 (tt) REVERT: B 336 GLU cc_start: 0.6997 (tp30) cc_final: 0.6453 (pm20) REVERT: B 398 VAL cc_start: 0.6689 (OUTLIER) cc_final: 0.6433 (m) outliers start: 21 outliers final: 14 residues processed: 143 average time/residue: 0.2227 time to fit residues: 45.8674 Evaluate side-chains 127 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 417 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 674 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 195 HIS ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.128870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.109341 restraints weight = 58175.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.112313 restraints weight = 33693.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.114157 restraints weight = 21885.381| |-----------------------------------------------------------------------------| r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10643 Z= 0.142 Angle : 0.725 16.449 14500 Z= 0.360 Chirality : 0.050 0.475 1573 Planarity : 0.005 0.058 1856 Dihedral : 6.344 57.848 1583 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 2.49 % Allowed : 16.36 % Favored : 81.16 % 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: -0.41 (0.26), residues: 410 sheet: -1.84 (0.49), residues: 95 loop : -2.03 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 461 HIS 0.021 0.002 HIS A 417 PHE 0.040 0.002 PHE A 72 TYR 0.025 0.002 TYR A 50 ARG 0.009 0.001 ARG A 465 Details of bonding type rmsd link_NAG-ASN : bond 0.00794 ( 7) link_NAG-ASN : angle 4.06704 ( 21) link_BETA1-4 : bond 0.02722 ( 2) link_BETA1-4 : angle 7.41930 ( 6) hydrogen bonds : bond 0.04455 ( 336) hydrogen bonds : angle 5.86281 ( 951) SS BOND : bond 0.00301 ( 13) SS BOND : angle 0.96832 ( 26) covalent geometry : bond 0.00306 (10621) covalent geometry : angle 0.69185 (14447) *********************** 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 155 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: A 123 MET cc_start: 0.6589 (mmp) cc_final: 0.5673 (mmt) REVERT: A 152 MET cc_start: 0.4728 (mmt) cc_final: 0.3700 (mmt) REVERT: A 180 TYR cc_start: 0.7483 (t80) cc_final: 0.7144 (t80) REVERT: A 270 MET cc_start: 0.3516 (tpt) cc_final: 0.2700 (tpt) REVERT: A 408 MET cc_start: 0.6196 (tmm) cc_final: 0.5782 (tmm) REVERT: A 421 MET cc_start: 0.6353 (ppp) cc_final: 0.6106 (ppp) REVERT: B 243 ILE cc_start: 0.5500 (pt) cc_final: 0.4949 (pt) REVERT: B 398 VAL cc_start: 0.6837 (OUTLIER) cc_final: 0.6610 (m) REVERT: B 615 GLU cc_start: 0.7522 (mp0) cc_final: 0.7280 (mp0) outliers start: 28 outliers final: 14 residues processed: 145 average time/residue: 0.2269 time to fit residues: 47.4898 Evaluate side-chains 125 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 333 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 556 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.122675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.101136 restraints weight = 51475.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.104182 restraints weight = 31060.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.106209 restraints weight = 21069.527| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10643 Z= 0.171 Angle : 0.737 16.324 14500 Z= 0.371 Chirality : 0.050 0.470 1573 Planarity : 0.005 0.058 1856 Dihedral : 6.283 57.630 1583 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.93 % Allowed : 17.60 % Favored : 79.47 % 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: -2.22 (0.22), residues: 1269 helix: -0.51 (0.25), residues: 412 sheet: -1.93 (0.50), residues: 93 loop : -2.05 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 461 HIS 0.008 0.002 HIS A 34 PHE 0.024 0.002 PHE B 388 TYR 0.023 0.002 TYR A 50 ARG 0.007 0.001 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00777 ( 7) link_NAG-ASN : angle 3.97243 ( 21) link_BETA1-4 : bond 0.02800 ( 2) link_BETA1-4 : angle 7.34860 ( 6) hydrogen bonds : bond 0.04510 ( 336) hydrogen bonds : angle 5.81437 ( 951) SS BOND : bond 0.00420 ( 13) SS BOND : angle 0.97829 ( 26) covalent geometry : bond 0.00380 (10621) covalent geometry : angle 0.70538 (14447) *********************** 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 161 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.103 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 152 MET cc_start: 0.4684 (mmt) cc_final: 0.3340 (mmt) REVERT: A 180 TYR cc_start: 0.8038 (t80) cc_final: 0.7612 (t80) REVERT: A 270 MET cc_start: 0.3516 (tpt) cc_final: 0.2537 (tpt) REVERT: A 408 MET cc_start: 0.6632 (tmm) cc_final: 0.6231 (tmm) REVERT: A 552 LYS cc_start: 0.7912 (ptpp) cc_final: 0.7515 (ptpp) REVERT: B 22 ARG cc_start: 0.4320 (tpp80) cc_final: 0.3474 (tpt170) REVERT: B 398 VAL cc_start: 0.6908 (OUTLIER) cc_final: 0.6699 (m) REVERT: B 615 GLU cc_start: 0.7699 (mp0) cc_final: 0.7457 (mp0) outliers start: 33 outliers final: 24 residues processed: 149 average time/residue: 0.2000 time to fit residues: 44.1247 Evaluate side-chains 140 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 59 VAL 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 295 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 588 PHE 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 303 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 556 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 111 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 122 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.122015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.100199 restraints weight = 51728.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.103149 restraints weight = 31302.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.105117 restraints weight = 21378.949| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10643 Z= 0.138 Angle : 0.730 16.294 14500 Z= 0.360 Chirality : 0.050 0.452 1573 Planarity : 0.005 0.055 1856 Dihedral : 6.166 56.339 1583 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.58 % Allowed : 19.64 % Favored : 77.78 % 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: -2.10 (0.23), residues: 1269 helix: -0.37 (0.25), residues: 407 sheet: -1.82 (0.50), residues: 103 loop : -1.99 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 461 HIS 0.010 0.001 HIS B 34 PHE 0.023 0.002 PHE B 388 TYR 0.016 0.001 TYR A 385 ARG 0.005 0.000 ARG B 404 Details of bonding type rmsd link_NAG-ASN : bond 0.00756 ( 7) link_NAG-ASN : angle 3.94362 ( 21) link_BETA1-4 : bond 0.02878 ( 2) link_BETA1-4 : angle 7.30570 ( 6) hydrogen bonds : bond 0.04299 ( 336) hydrogen bonds : angle 5.68276 ( 951) SS BOND : bond 0.00348 ( 13) SS BOND : angle 1.01736 ( 26) covalent geometry : bond 0.00294 (10621) covalent geometry : angle 0.69840 (14447) *********************** 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 154 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.147 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 123 MET cc_start: 0.6748 (mmp) cc_final: 0.6129 (mmt) REVERT: A 180 TYR cc_start: 0.8136 (t80) cc_final: 0.7724 (t80) REVERT: A 190 MET cc_start: 0.8340 (tmm) cc_final: 0.8134 (tmm) REVERT: A 408 MET cc_start: 0.6766 (tmm) cc_final: 0.6326 (tmm) REVERT: A 474 MET cc_start: 0.6037 (ppp) cc_final: 0.5336 (mmm) REVERT: B 22 ARG cc_start: 0.4212 (tpp80) cc_final: 0.3633 (tpt-90) REVERT: B 132 ASN cc_start: 0.3023 (OUTLIER) cc_final: 0.2753 (m110) REVERT: B 398 VAL cc_start: 0.6691 (OUTLIER) cc_final: 0.6472 (m) REVERT: B 615 GLU cc_start: 0.7669 (mp0) cc_final: 0.7402 (mp0) outliers start: 29 outliers final: 19 residues processed: 147 average time/residue: 0.1976 time to fit residues: 43.1272 Evaluate side-chains 131 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 588 PHE 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 270 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 398 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 195 HIS ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.120724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.098879 restraints weight = 52634.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.101881 restraints weight = 31250.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.103894 restraints weight = 21150.158| |-----------------------------------------------------------------------------| r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10643 Z= 0.141 Angle : 0.731 16.225 14500 Z= 0.365 Chirality : 0.050 0.451 1573 Planarity : 0.005 0.055 1856 Dihedral : 6.044 56.024 1583 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.40 % Allowed : 19.91 % 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: -2.10 (0.23), residues: 1269 helix: -0.40 (0.25), residues: 411 sheet: -1.74 (0.51), residues: 103 loop : -1.99 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 461 HIS 0.021 0.002 HIS A 195 PHE 0.023 0.002 PHE B 388 TYR 0.016 0.001 TYR A 237 ARG 0.004 0.000 ARG B 404 Details of bonding type rmsd link_NAG-ASN : bond 0.00739 ( 7) link_NAG-ASN : angle 3.88198 ( 21) link_BETA1-4 : bond 0.02780 ( 2) link_BETA1-4 : angle 7.26428 ( 6) hydrogen bonds : bond 0.04378 ( 336) hydrogen bonds : angle 5.69385 ( 951) SS BOND : bond 0.00386 ( 13) SS BOND : angle 1.15765 ( 26) covalent geometry : bond 0.00308 (10621) covalent geometry : angle 0.69954 (14447) *********************** 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 142 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.6864 (mmp) cc_final: 0.5814 (mmt) REVERT: A 176 LEU cc_start: 0.7822 (mt) cc_final: 0.7313 (mt) REVERT: A 180 TYR cc_start: 0.8284 (t80) cc_final: 0.7841 (t80) REVERT: A 270 MET cc_start: 0.3580 (tpt) cc_final: 0.3195 (tpp) REVERT: A 355 ASP cc_start: 0.6509 (t0) cc_final: 0.6209 (t0) REVERT: A 408 MET cc_start: 0.6789 (tmm) cc_final: 0.6420 (tmm) REVERT: A 421 MET cc_start: 0.6818 (ppp) cc_final: 0.6554 (ppp) REVERT: A 474 MET cc_start: 0.5936 (ppp) cc_final: 0.5379 (mmm) REVERT: A 532 ILE cc_start: 0.8145 (mp) cc_final: 0.7921 (mp) REVERT: B 132 ASN cc_start: 0.3044 (OUTLIER) cc_final: 0.2774 (m110) REVERT: B 262 TYR cc_start: 0.4753 (m-10) cc_final: 0.4015 (m-10) REVERT: B 398 VAL cc_start: 0.6990 (OUTLIER) cc_final: 0.6748 (m) REVERT: B 615 GLU cc_start: 0.7758 (mp0) cc_final: 0.7472 (mp0) outliers start: 27 outliers final: 20 residues processed: 135 average time/residue: 0.1976 time to fit residues: 40.2338 Evaluate side-chains 131 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 93 VAL Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 295 ASP 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 588 PHE 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 270 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 398 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 559 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 105 optimal weight: 0.0060 chunk 81 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 0.0030 chunk 64 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 overall best weight: 1.2010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 508 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 410 GLN B 559 GLN ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.118618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.096255 restraints weight = 52190.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.099184 restraints weight = 31311.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.101108 restraints weight = 21398.140| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10643 Z= 0.147 Angle : 0.742 16.586 14500 Z= 0.370 Chirality : 0.050 0.448 1573 Planarity : 0.005 0.054 1856 Dihedral : 5.988 56.279 1583 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 2.76 % Allowed : 20.09 % Favored : 77.16 % 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: -2.08 (0.23), residues: 1269 helix: -0.36 (0.25), residues: 412 sheet: -1.90 (0.53), residues: 97 loop : -1.97 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 461 HIS 0.007 0.001 HIS A 417 PHE 0.034 0.002 PHE B 425 TYR 0.016 0.001 TYR A 237 ARG 0.006 0.000 ARG B 563 Details of bonding type rmsd link_NAG-ASN : bond 0.00730 ( 7) link_NAG-ASN : angle 3.83090 ( 21) link_BETA1-4 : bond 0.03277 ( 2) link_BETA1-4 : angle 7.37987 ( 6) hydrogen bonds : bond 0.04412 ( 336) hydrogen bonds : angle 5.66589 ( 951) SS BOND : bond 0.00361 ( 13) SS BOND : angle 1.05001 ( 26) covalent geometry : bond 0.00317 (10621) covalent geometry : angle 0.71143 (14447) *********************** 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 149 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7112 (mmp) cc_final: 0.6215 (mmt) REVERT: A 176 LEU cc_start: 0.7876 (mt) cc_final: 0.7665 (mt) REVERT: A 180 TYR cc_start: 0.8392 (t80) cc_final: 0.7845 (t80) REVERT: A 270 MET cc_start: 0.3582 (tpt) cc_final: 0.3332 (tpt) REVERT: A 355 ASP cc_start: 0.6545 (t0) cc_final: 0.6206 (t0) REVERT: A 408 MET cc_start: 0.7041 (tmm) cc_final: 0.6703 (tmm) REVERT: A 421 MET cc_start: 0.6876 (ppp) cc_final: 0.6644 (ppp) REVERT: B 132 ASN cc_start: 0.3154 (OUTLIER) cc_final: 0.2891 (m110) REVERT: B 615 GLU cc_start: 0.7897 (mp0) cc_final: 0.7611 (mp0) outliers start: 31 outliers final: 24 residues processed: 138 average time/residue: 0.2396 time to fit residues: 50.7520 Evaluate side-chains 133 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 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 93 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 291 ILE Chi-restraints excluded: chain A residue 295 ASP 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 A residue 508 ASN Chi-restraints excluded: chain A residue 588 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 90 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 476 CYS Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 534 CYS Chi-restraints excluded: chain B residue 556 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 76 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 72 optimal weight: 0.0270 chunk 58 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 508 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.118141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.096113 restraints weight = 53233.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.099079 restraints weight = 31210.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.101045 restraints weight = 20993.551| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10643 Z= 0.140 Angle : 0.753 16.302 14500 Z= 0.375 Chirality : 0.050 0.443 1573 Planarity : 0.005 0.054 1856 Dihedral : 5.916 55.934 1583 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.58 % Allowed : 20.44 % Favored : 76.98 % 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: -2.05 (0.23), residues: 1269 helix: -0.31 (0.25), residues: 407 sheet: -1.95 (0.58), residues: 84 loop : -1.97 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 461 HIS 0.006 0.001 HIS A 417 PHE 0.036 0.002 PHE B 425 TYR 0.016 0.001 TYR A 385 ARG 0.007 0.000 ARG B 563 Details of bonding type rmsd link_NAG-ASN : bond 0.00734 ( 7) link_NAG-ASN : angle 3.80937 ( 21) link_BETA1-4 : bond 0.03036 ( 2) link_BETA1-4 : angle 7.23910 ( 6) hydrogen bonds : bond 0.04389 ( 336) hydrogen bonds : angle 5.66779 ( 951) SS BOND : bond 0.00325 ( 13) SS BOND : angle 0.92309 ( 26) covalent geometry : bond 0.00299 (10621) covalent geometry : angle 0.72390 (14447) *********************** 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 136 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 1.312 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 123 MET cc_start: 0.7083 (mmp) cc_final: 0.6167 (mmt) REVERT: A 150 ASN cc_start: 0.8362 (p0) cc_final: 0.8109 (p0) REVERT: A 176 LEU cc_start: 0.7830 (mt) cc_final: 0.7620 (mt) REVERT: A 180 TYR cc_start: 0.8256 (t80) cc_final: 0.7715 (t80) REVERT: A 270 MET cc_start: 0.3679 (tpt) cc_final: 0.3368 (tpt) REVERT: A 355 ASP cc_start: 0.6518 (t0) cc_final: 0.6225 (t0) REVERT: A 408 MET cc_start: 0.6996 (tmm) cc_final: 0.6606 (tmm) REVERT: A 421 MET cc_start: 0.6958 (ppp) cc_final: 0.6704 (ppp) REVERT: A 592 TYR cc_start: 0.8053 (t80) cc_final: 0.7768 (t80) REVERT: B 132 ASN cc_start: 0.3218 (OUTLIER) cc_final: 0.2745 (m-40) REVERT: B 325 PHE cc_start: 0.1669 (m-80) cc_final: 0.0366 (m-80) REVERT: B 336 GLU cc_start: 0.7190 (tp30) cc_final: 0.6964 (pm20) outliers start: 29 outliers final: 22 residues processed: 127 average time/residue: 0.1959 time to fit residues: 38.4575 Evaluate side-chains 125 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 93 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 291 ILE Chi-restraints excluded: chain A residue 295 ASP 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 A residue 508 ASN Chi-restraints excluded: chain A residue 588 PHE 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 270 THR 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 506 VAL Chi-restraints excluded: chain B residue 559 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 38 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 95 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 195 HIS ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 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 = 0.4615 r_free = 0.4615 target = 0.117843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.095959 restraints weight = 53173.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.098834 restraints weight = 31620.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.100811 restraints weight = 21488.797| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10643 Z= 0.139 Angle : 0.768 16.249 14500 Z= 0.385 Chirality : 0.050 0.443 1573 Planarity : 0.005 0.054 1856 Dihedral : 5.883 55.507 1583 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.90 % Favored : 91.02 % Rotamer: Outliers : 1.87 % Allowed : 20.98 % Favored : 77.16 % 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: -2.05 (0.23), residues: 1269 helix: -0.29 (0.25), residues: 406 sheet: -1.81 (0.58), residues: 84 loop : -1.99 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 461 HIS 0.016 0.002 HIS A 195 PHE 0.037 0.002 PHE B 425 TYR 0.016 0.001 TYR A 385 ARG 0.007 0.000 ARG B 563 Details of bonding type rmsd link_NAG-ASN : bond 0.00730 ( 7) link_NAG-ASN : angle 3.78461 ( 21) link_BETA1-4 : bond 0.02938 ( 2) link_BETA1-4 : angle 7.22056 ( 6) hydrogen bonds : bond 0.04385 ( 336) hydrogen bonds : angle 5.65658 ( 951) SS BOND : bond 0.00343 ( 13) SS BOND : angle 0.95807 ( 26) covalent geometry : bond 0.00301 (10621) covalent geometry : angle 0.74030 (14447) ********************** 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 to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8384 (mm110) REVERT: A 123 MET cc_start: 0.7096 (mmp) cc_final: 0.6170 (mmt) REVERT: A 150 ASN cc_start: 0.8412 (p0) cc_final: 0.8164 (p0) REVERT: A 176 LEU cc_start: 0.7874 (mt) cc_final: 0.7365 (mt) REVERT: A 180 TYR cc_start: 0.8378 (t80) cc_final: 0.7815 (t80) REVERT: A 270 MET cc_start: 0.3686 (tpt) cc_final: 0.3385 (tpt) REVERT: A 355 ASP cc_start: 0.6486 (t0) cc_final: 0.6169 (t0) REVERT: A 408 MET cc_start: 0.7065 (tmm) cc_final: 0.6733 (tmm) REVERT: A 421 MET cc_start: 0.6927 (ppp) cc_final: 0.6688 (ppp) REVERT: B 132 ASN cc_start: 0.3064 (OUTLIER) cc_final: 0.2569 (m-40) REVERT: B 325 PHE cc_start: 0.1770 (m-80) cc_final: 0.0766 (m-80) outliers start: 21 outliers final: 17 residues processed: 120 average time/residue: 0.2043 time to fit residues: 37.9900 Evaluate side-chains 121 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 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 A residue 508 ASN Chi-restraints excluded: chain A residue 588 PHE 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 270 THR Chi-restraints excluded: chain B residue 298 THR 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.7678 > 50: distance: 105 - 127: 14.438 distance: 112 - 135: 7.758 distance: 117 - 141: 4.886 distance: 121 - 127: 14.837 distance: 127 - 128: 31.490 distance: 128 - 129: 30.735 distance: 128 - 131: 31.974 distance: 129 - 130: 32.817 distance: 129 - 135: 12.323 distance: 131 - 132: 26.849 distance: 132 - 133: 19.654 distance: 132 - 134: 17.468 distance: 135 - 136: 7.733 distance: 136 - 137: 12.186 distance: 136 - 139: 21.701 distance: 137 - 138: 18.954 distance: 137 - 141: 11.052 distance: 139 - 140: 11.867 distance: 141 - 142: 3.907 distance: 142 - 143: 15.417 distance: 142 - 145: 7.009 distance: 143 - 144: 11.402 distance: 143 - 148: 5.910 distance: 145 - 146: 9.194 distance: 145 - 147: 12.781 distance: 148 - 149: 6.152 distance: 149 - 150: 5.710 distance: 150 - 151: 20.026 distance: 150 - 152: 25.833 distance: 152 - 153: 5.701 distance: 153 - 154: 19.458 distance: 153 - 156: 12.393 distance: 154 - 155: 22.762 distance: 154 - 161: 25.045 distance: 156 - 157: 32.625 distance: 157 - 158: 18.248 distance: 158 - 159: 10.026 distance: 159 - 160: 6.698 distance: 161 - 162: 28.588 distance: 162 - 163: 20.774 distance: 162 - 165: 23.157 distance: 163 - 164: 32.059 distance: 163 - 167: 23.852 distance: 165 - 166: 20.225 distance: 167 - 168: 34.751 distance: 168 - 169: 37.541 distance: 168 - 171: 41.676 distance: 169 - 170: 43.463 distance: 169 - 176: 12.310 distance: 171 - 172: 27.748 distance: 172 - 173: 13.366 distance: 173 - 174: 20.887 distance: 173 - 175: 16.835 distance: 176 - 177: 20.471 distance: 176 - 182: 19.660 distance: 177 - 178: 22.918 distance: 177 - 180: 20.980 distance: 178 - 179: 36.132 distance: 178 - 183: 31.283 distance: 179 - 211: 19.200 distance: 180 - 181: 37.042 distance: 181 - 182: 37.090 distance: 183 - 184: 14.488 distance: 184 - 185: 18.372 distance: 184 - 187: 29.792 distance: 185 - 186: 14.709 distance: 185 - 197: 19.060 distance: 186 - 218: 9.967 distance: 187 - 188: 15.850 distance: 188 - 189: 11.236 distance: 188 - 190: 20.649 distance: 189 - 191: 6.906 distance: 190 - 192: 33.236 distance: 190 - 193: 13.957 distance: 191 - 192: 25.143 distance: 192 - 194: 19.475 distance: 193 - 195: 14.607 distance: 194 - 196: 7.128 distance: 195 - 196: 6.623 distance: 197 - 198: 17.681 distance: 198 - 199: 27.416 distance: 198 - 201: 17.739 distance: 199 - 200: 21.313 distance: 199 - 204: 11.931 distance: 200 - 225: 10.642 distance: 201 - 202: 15.084 distance: 201 - 203: 19.547