Starting phenix.real_space_refine on Thu Jul 2 02:22:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wpz_32693/07_2026/7wpz_32693.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpz_32693/07_2026/7wpz_32693.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7wpz_32693/07_2026/7wpz_32693.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wpz_32693/07_2026/7wpz_32693.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wpz_32693/07_2026/7wpz_32693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpz_32693/07_2026/7wpz_32693.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wpz_32693/07_2026/7wpz_32693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpz_32693/07_2026/7wpz_32693.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.007 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 31 5.16 5 C 3672 2.51 5 N 1016 2.21 5 O 1037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5756 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4361 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PTRANS': 24, 'TRANS': 570} Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 671 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLU:plan': 36, 'ASP:plan': 23, 'GLN:plan1': 10, 'ASN:plan1': 5, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 284 Chain: "B" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1194 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 11, 'TRANS': 180} Chain breaks: 3 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'ASN:plan1': 8, 'PHE:plan': 5, 'ASP:plan': 7, 'ARG:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 5, 'TYR:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 159 Chain: "E" 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 chiralities: 2 Chain: "J" 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 chiralities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 1 Time building chain proxies: 0.97, per 1000 atoms: 0.17 Number of scatterers: 5756 At special positions: 0 Unit cell: (88.56, 94.3, 117.26, 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 31 16.00 O 1037 8.00 N 1016 7.00 C 3672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 142 " distance=2.20 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.11 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 411 " distance=2.08 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 583 " distance=2.07 Simple disulfide: pdb=" SG CYS B 506 " - pdb=" SG CYS B 527 " distance=2.02 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 701 " - " ASN A 329 " " NAG A 702 " - " ASN A 546 " " NAG A 703 " - " ASN A 91 " " NAG B 601 " - " ASN B 489 " " NAG C 1 " - " ASN A 54 " " NAG D 1 " - " ASN A 104 " " NAG E 1 " - " ASN A 280 " " NAG J 1 " - " ASN A 432 " Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 195.6 milliseconds 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1486 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 58.7% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 21 through 53 Processing helix chain 'A' and resid 56 through 82 removed outlier: 4.082A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 110 through 130 Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.911A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.824A pdb=" N MET A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.994A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (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 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' 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 331 removed outlier: 3.500A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 removed outlier: 4.473A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 414 removed outlier: 3.599A 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 447 removed outlier: 3.706A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) 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 485 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 534 removed outlier: 3.531A pdb=" N PHE A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.855A pdb=" N ILE A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 600 Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.072A pdb=" N GLN A 615 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.657A pdb=" N VAL B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 453 through 460 removed outlier: 4.424A pdb=" N SER B 458 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 524 through 533 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.365A 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 404 through 408 removed outlier: 3.561A pdb=" N LYS B 404 " --> pdb=" O TRP B 449 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N HIS B 485 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 411 through 412 removed outlier: 6.101A pdb=" N CYS B 411 " --> pdb=" O CYS B 583 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 513 through 514 removed outlier: 6.607A pdb=" N SER B 553 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS B 506 " --> pdb=" O ARG B 551 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG B 551 " --> pdb=" O CYS B 506 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR B 508 " --> pdb=" O PRO B 549 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 942 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: 0.59 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1245 1.33 - 1.46: 2088 1.46 - 1.60: 2530 1.60 - 1.73: 1 1.73 - 1.87: 49 Bond restraints: 5913 Sorted by residual: bond pdb=" CA LEU A 491 " pdb=" C LEU A 491 " ideal model delta sigma weight residual 1.522 1.566 -0.044 8.40e-03 1.42e+04 2.71e+01 bond pdb=" CA ASN A 546 " pdb=" C ASN A 546 " ideal model delta sigma weight residual 1.525 1.579 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" NE ARG B 483 " pdb=" CZ ARG B 483 " ideal model delta sigma weight residual 1.326 1.368 -0.042 1.10e-02 8.26e+03 1.46e+01 bond pdb=" N PRO A 492 " pdb=" CD PRO A 492 " ideal model delta sigma weight residual 1.473 1.420 0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 5908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 7829 3.35 - 6.70: 242 6.70 - 10.05: 12 10.05 - 13.41: 1 13.41 - 16.76: 1 Bond angle restraints: 8085 Sorted by residual: angle pdb=" N ILE B 494 " pdb=" CA ILE B 494 " pdb=" C ILE B 494 " ideal model delta sigma weight residual 109.34 92.58 16.76 2.08e+00 2.31e-01 6.49e+01 angle pdb=" C GLY A 537 " pdb=" N PRO A 538 " pdb=" CA PRO A 538 " ideal model delta sigma weight residual 119.76 127.80 -8.04 1.03e+00 9.43e-01 6.09e+01 angle pdb=" C GLU A 489 " pdb=" N PRO A 490 " pdb=" CA PRO A 490 " ideal model delta sigma weight residual 119.56 126.92 -7.36 1.02e+00 9.61e-01 5.21e+01 angle pdb=" C GLU A 335 " pdb=" N PRO A 336 " pdb=" CA PRO A 336 " ideal model delta sigma weight residual 119.85 126.95 -7.10 1.01e+00 9.80e-01 4.94e+01 angle pdb=" C GLU B 576 " pdb=" N PRO B 577 " pdb=" CA PRO B 577 " ideal model delta sigma weight residual 119.78 126.84 -7.06 1.03e+00 9.43e-01 4.70e+01 ... (remaining 8080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 3175 15.46 - 30.93: 107 30.93 - 46.39: 24 46.39 - 61.86: 9 61.86 - 77.32: 3 Dihedral angle restraints: 3318 sinusoidal: 1012 harmonic: 2306 Sorted by residual: dihedral pdb=" N ILE B 494 " pdb=" C ILE B 494 " pdb=" CA ILE B 494 " pdb=" CB ILE B 494 " ideal model delta harmonic sigma weight residual 123.40 106.22 17.18 0 2.50e+00 1.60e-01 4.72e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -124.14 38.14 1 1.00e+01 1.00e-02 2.05e+01 dihedral pdb=" C ILE B 494 " pdb=" N ILE B 494 " pdb=" CA ILE B 494 " pdb=" CB ILE B 494 " ideal model delta harmonic sigma weight residual -122.00 -110.76 -11.24 0 2.50e+00 1.60e-01 2.02e+01 ... (remaining 3315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.232: 862 0.232 - 0.463: 37 0.463 - 0.695: 0 0.695 - 0.927: 1 0.927 - 1.159: 1 Chirality restraints: 901 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.45e+02 chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.60 -0.20 2.00e-02 2.50e+03 9.87e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.25e+01 ... (remaining 898 not shown) Planarity restraints: 1055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 491 " 0.018 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LEU A 491 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU A 491 " 0.025 2.00e-02 2.50e+03 pdb=" N PRO A 492 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " -0.027 2.00e-02 2.50e+03 2.77e-02 9.58e+00 pdb=" CG ASN A 329 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " 0.043 2.00e-02 2.50e+03 pdb=" C1 NAG A 701 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 91 " -0.022 2.00e-02 2.50e+03 2.68e-02 8.98e+00 pdb=" CG ASN A 91 " -0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN A 91 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 91 " 0.045 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " -0.032 2.00e-02 2.50e+03 ... (remaining 1052 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 2433 2.93 - 3.42: 5498 3.42 - 3.91: 9550 3.91 - 4.41: 10552 4.41 - 4.90: 16754 Nonbonded interactions: 44787 Sorted by model distance: nonbonded pdb=" N VAL A 108 " pdb=" N LEU A 109 " model vdw 2.431 2.560 nonbonded pdb=" N ALA B 523 " pdb=" O ALA B 523 " model vdw 2.519 2.496 nonbonded pdb=" N LYS B 562 " pdb=" O LYS B 562 " model vdw 2.581 2.496 nonbonded pdb=" O GLN A 239 " pdb=" ND2 ASN A 599 " model vdw 2.581 3.120 nonbonded pdb=" N ARG B 467 " pdb=" N ILE B 468 " model vdw 2.587 2.560 ... (remaining 44782 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 'D' selection = chain 'E' selection = chain 'J' } 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: 0.930 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.520 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 : 0.014 0.172 5934 Z= 0.791 Angle : 1.477 31.162 8142 Z= 0.981 Chirality : 0.111 1.159 901 Planarity : 0.006 0.038 1047 Dihedral : 9.565 77.321 1814 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.19 % Favored : 97.43 % Rotamer: Outliers : 0.74 % Allowed : 0.99 % Favored : 98.26 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.27), residues: 777 helix: -0.10 (0.23), residues: 405 sheet: 0.71 (0.69), residues: 50 loop : 0.05 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 161 TYR 0.035 0.005 TYR A 217 PHE 0.024 0.004 PHE A 592 TRP 0.030 0.005 TRP A 328 HIS 0.005 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.01343 / 0.76 ( 5913) covalent geometry : angle 1.40915 / 0.97 ( 8085) SS BOND : bond 0.08177 / 4.34 ( 6) SS BOND : angle 3.64828 / 2.46 ( 12) hydrogen bonds : bond 0.20180 / 14.13 ( 334) hydrogen bonds : angle 6.91116 / 5.16 ( 942) link_ALPHA1-3 : bond 0.07174 / 3.78 ( 1) link_ALPHA1-3 : angle 3.78688 / 1.74 ( 3) link_ALPHA1-6 : bond 0.07594 / 4.00 ( 1) link_ALPHA1-6 : angle 1.62593 / 0.71 ( 3) link_BETA1-4 : bond 0.07650 / 4.12 ( 5) link_BETA1-4 : angle 3.68366 / 2.70 ( 15) link_NAG-ASN : bond 0.06766 / 4.19 ( 8) link_NAG-ASN : angle 7.37181 / 3.34 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.7652 (ttp) cc_final: 0.7421 (ttp) REVERT: A 223 MET cc_start: 0.7557 (mtm) cc_final: 0.7317 (mtt) REVERT: A 510 TYR cc_start: 0.6825 (m-80) cc_final: 0.6513 (m-10) REVERT: B 474 ASN cc_start: 0.7697 (t0) cc_final: 0.7386 (t0) REVERT: B 475 GLN cc_start: 0.8105 (tt0) cc_final: 0.7541 (tt0) outliers start: 3 outliers final: 0 residues processed: 123 average time/residue: 0.0789 time to fit residues: 12.4421 Evaluate side-chains 67 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 HIS A 330 ASN A 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.125085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.111097 restraints weight = 12096.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.113444 restraints weight = 6201.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.114945 restraints weight = 3765.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115929 restraints weight = 2579.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116543 restraints weight = 1946.368| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5934 Z= 0.157 Angle : 0.669 11.023 8142 Z= 0.345 Chirality : 0.043 0.202 901 Planarity : 0.005 0.042 1047 Dihedral : 4.035 14.020 847 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 0.90 % Favored : 98.97 % Rotamer: Outliers : 1.49 % Allowed : 8.44 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.29), residues: 777 helix: 1.44 (0.25), residues: 405 sheet: 1.27 (0.63), residues: 54 loop : 0.20 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 219 TYR 0.027 0.002 TYR A 315 PHE 0.024 0.002 PHE A 73 TRP 0.022 0.002 TRP A 163 HIS 0.003 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 ( 5913) covalent geometry : angle 0.63000 / 0.34 ( 8085) SS BOND : bond 0.00393 / 0.19 ( 6) SS BOND : angle 2.72699 / 1.51 ( 12) hydrogen bonds : bond 0.06202 / 4.21 ( 334) hydrogen bonds : angle 4.90138 / 3.65 ( 942) link_ALPHA1-3 : bond 0.00781 / 0.41 ( 1) link_ALPHA1-3 : angle 1.68965 / 0.89 ( 3) link_ALPHA1-6 : bond 0.00651 / 0.34 ( 1) link_ALPHA1-6 : angle 1.81850 / 0.90 ( 3) link_BETA1-4 : bond 0.00702 / 0.35 ( 5) link_BETA1-4 : angle 1.98712 / 1.43 ( 15) link_NAG-ASN : bond 0.00641 / 0.42 ( 8) link_NAG-ASN : angle 3.34171 / 2.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6695 (mmm) REVERT: B 474 ASN cc_start: 0.7662 (t0) cc_final: 0.7332 (t0) outliers start: 6 outliers final: 1 residues processed: 75 average time/residue: 0.0597 time to fit residues: 6.2995 Evaluate side-chains 63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 152 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.0970 chunk 17 optimal weight: 0.0570 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106525 restraints weight = 12286.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.108898 restraints weight = 6227.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110425 restraints weight = 3782.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111346 restraints weight = 2611.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112053 restraints weight = 2018.600| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5934 Z= 0.118 Angle : 0.522 5.936 8142 Z= 0.272 Chirality : 0.041 0.145 901 Planarity : 0.004 0.030 1047 Dihedral : 3.674 19.807 847 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.06 % Favored : 97.81 % Rotamer: Outliers : 1.24 % Allowed : 11.41 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.30), residues: 777 helix: 2.02 (0.25), residues: 401 sheet: 1.48 (0.64), residues: 52 loop : 0.13 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.018 0.001 TYR A 385 PHE 0.017 0.002 PHE A 592 TRP 0.017 0.001 TRP A 163 HIS 0.002 0.000 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.12 ( 5913) covalent geometry : angle 0.50135 / 0.27 ( 8085) SS BOND : bond 0.00341 / 0.23 ( 6) SS BOND : angle 1.33925 / 0.85 ( 12) hydrogen bonds : bond 0.04905 / 3.32 ( 334) hydrogen bonds : angle 4.43194 / 3.28 ( 942) link_ALPHA1-3 : bond 0.00620 / 0.33 ( 1) link_ALPHA1-3 : angle 1.35060 / 0.72 ( 3) link_ALPHA1-6 : bond 0.00939 / 0.49 ( 1) link_ALPHA1-6 : angle 1.21491 / 0.65 ( 3) link_BETA1-4 : bond 0.00554 / 0.31 ( 5) link_BETA1-4 : angle 1.33337 / 1.01 ( 15) link_NAG-ASN : bond 0.00442 / 0.28 ( 8) link_NAG-ASN : angle 2.32595 / 1.54 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 480 MET cc_start: 0.8345 (mtp) cc_final: 0.8090 (mtp) REVERT: B 474 ASN cc_start: 0.7596 (t0) cc_final: 0.7180 (t0) REVERT: B 500 TYR cc_start: 0.5537 (m-80) cc_final: 0.5293 (m-80) outliers start: 5 outliers final: 3 residues processed: 72 average time/residue: 0.0683 time to fit residues: 6.8258 Evaluate side-chains 69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain B residue 442 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.101755 restraints weight = 12381.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.103845 restraints weight = 6486.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.105242 restraints weight = 4030.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.106160 restraints weight = 2828.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106737 restraints weight = 2176.035| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5934 Z= 0.126 Angle : 0.526 5.886 8142 Z= 0.268 Chirality : 0.041 0.144 901 Planarity : 0.004 0.034 1047 Dihedral : 3.557 14.928 847 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.54 % Favored : 98.33 % Rotamer: Outliers : 1.74 % Allowed : 12.41 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.31), residues: 777 helix: 2.05 (0.25), residues: 412 sheet: 1.28 (0.64), residues: 52 loop : 0.21 (0.38), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 575 TYR 0.016 0.001 TYR B 550 PHE 0.014 0.001 PHE A 592 TRP 0.017 0.001 TRP A 163 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 5913) covalent geometry : angle 0.50622 / 0.26 ( 8085) SS BOND : bond 0.00399 / 0.21 ( 6) SS BOND : angle 1.40916 / 0.82 ( 12) hydrogen bonds : bond 0.04730 / 3.20 ( 334) hydrogen bonds : angle 4.32218 / 3.21 ( 942) link_ALPHA1-3 : bond 0.00307 / 0.16 ( 1) link_ALPHA1-3 : angle 1.42421 / 0.73 ( 3) link_ALPHA1-6 : bond 0.00356 / 0.19 ( 1) link_ALPHA1-6 : angle 1.67569 / 0.89 ( 3) link_BETA1-4 : bond 0.00315 / 0.17 ( 5) link_BETA1-4 : angle 1.41571 / 1.04 ( 15) link_NAG-ASN : bond 0.00327 / 0.20 ( 8) link_NAG-ASN : angle 2.16317 / 1.61 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 TYR cc_start: 0.8411 (m-80) cc_final: 0.7411 (m-80) REVERT: A 478 TRP cc_start: 0.8171 (m100) cc_final: 0.7963 (m100) REVERT: A 512 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: B 474 ASN cc_start: 0.7715 (t0) cc_final: 0.7364 (t0) REVERT: B 500 TYR cc_start: 0.5541 (m-80) cc_final: 0.5278 (m-80) outliers start: 7 outliers final: 6 residues processed: 79 average time/residue: 0.0692 time to fit residues: 7.4514 Evaluate side-chains 81 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 442 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 24 optimal weight: 0.0970 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.096705 restraints weight = 12818.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098758 restraints weight = 6712.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.100115 restraints weight = 4175.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100940 restraints weight = 2939.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.101572 restraints weight = 2297.189| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5934 Z= 0.141 Angle : 0.542 6.287 8142 Z= 0.276 Chirality : 0.042 0.147 901 Planarity : 0.004 0.035 1047 Dihedral : 3.632 15.645 847 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.96 % Favored : 96.91 % Rotamer: Outliers : 2.48 % Allowed : 11.41 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.31), residues: 777 helix: 2.05 (0.25), residues: 415 sheet: 1.07 (0.67), residues: 53 loop : 0.08 (0.39), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 575 TYR 0.014 0.002 TYR B 550 PHE 0.015 0.002 PHE A 592 TRP 0.017 0.002 TRP A 163 HIS 0.004 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 5913) covalent geometry : angle 0.52494 / 0.27 ( 8085) SS BOND : bond 0.00383 / 0.27 ( 6) SS BOND : angle 0.96161 / 0.68 ( 12) hydrogen bonds : bond 0.04982 / 3.38 ( 334) hydrogen bonds : angle 4.39957 / 3.27 ( 942) link_ALPHA1-3 : bond 0.00534 / 0.28 ( 1) link_ALPHA1-3 : angle 1.29995 / 0.70 ( 3) link_ALPHA1-6 : bond 0.00540 / 0.28 ( 1) link_ALPHA1-6 : angle 1.62023 / 0.89 ( 3) link_BETA1-4 : bond 0.00373 / 0.21 ( 5) link_BETA1-4 : angle 1.43528 / 1.07 ( 15) link_NAG-ASN : bond 0.00335 / 0.19 ( 8) link_NAG-ASN : angle 2.16319 / 1.61 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8359 (mt) REVERT: A 68 SER cc_start: 0.8688 (OUTLIER) cc_final: 0.8345 (m) REVERT: A 201 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8238 (t0) REVERT: A 207 TYR cc_start: 0.8487 (m-80) cc_final: 0.7575 (m-80) REVERT: A 512 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7603 (m-80) REVERT: B 474 ASN cc_start: 0.7812 (t0) cc_final: 0.7484 (t0) REVERT: B 500 TYR cc_start: 0.5583 (m-80) cc_final: 0.5357 (m-80) outliers start: 10 outliers final: 4 residues processed: 78 average time/residue: 0.0768 time to fit residues: 8.0630 Evaluate side-chains 79 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 442 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 485 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.094720 restraints weight = 12676.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.096726 restraints weight = 6623.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.098034 restraints weight = 4124.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098876 restraints weight = 2908.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.099434 restraints weight = 2261.984| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5934 Z= 0.140 Angle : 0.542 5.717 8142 Z= 0.272 Chirality : 0.041 0.144 901 Planarity : 0.004 0.034 1047 Dihedral : 3.677 16.348 847 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.23 % Allowed : 11.91 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.31), residues: 777 helix: 2.05 (0.25), residues: 415 sheet: 0.76 (0.68), residues: 53 loop : -0.14 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 192 TYR 0.016 0.002 TYR A 385 PHE 0.012 0.002 PHE A 525 TRP 0.017 0.001 TRP A 163 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 5913) covalent geometry : angle 0.52195 / 0.27 ( 8085) SS BOND : bond 0.00295 / 0.16 ( 6) SS BOND : angle 1.23711 / 0.86 ( 12) hydrogen bonds : bond 0.04922 / 3.35 ( 334) hydrogen bonds : angle 4.40085 / 3.27 ( 942) link_ALPHA1-3 : bond 0.00510 / 0.27 ( 1) link_ALPHA1-3 : angle 1.37303 / 0.70 ( 3) link_ALPHA1-6 : bond 0.00496 / 0.26 ( 1) link_ALPHA1-6 : angle 1.74494 / 0.95 ( 3) link_BETA1-4 : bond 0.00310 / 0.18 ( 5) link_BETA1-4 : angle 1.54980 / 1.17 ( 15) link_NAG-ASN : bond 0.00319 / 0.19 ( 8) link_NAG-ASN : angle 2.25628 / 1.72 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8151 (t-100) cc_final: 0.7676 (t-100) REVERT: A 68 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8399 (m) REVERT: A 207 TYR cc_start: 0.8450 (m-80) cc_final: 0.7626 (m-80) REVERT: A 512 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7624 (m-80) REVERT: B 474 ASN cc_start: 0.7859 (t0) cc_final: 0.7532 (t0) REVERT: B 500 TYR cc_start: 0.5615 (m-80) cc_final: 0.5390 (m-80) outliers start: 9 outliers final: 3 residues processed: 77 average time/residue: 0.0774 time to fit residues: 8.0022 Evaluate side-chains 75 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 442 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 74 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.104268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.090713 restraints weight = 12928.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.092615 restraints weight = 6767.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.093865 restraints weight = 4218.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.094646 restraints weight = 2988.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.095181 restraints weight = 2341.374| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5934 Z= 0.197 Angle : 0.623 5.838 8142 Z= 0.313 Chirality : 0.044 0.154 901 Planarity : 0.004 0.039 1047 Dihedral : 4.026 16.838 847 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.23 % Allowed : 11.91 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.30), residues: 777 helix: 1.75 (0.25), residues: 415 sheet: 0.55 (0.70), residues: 54 loop : -0.52 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 192 TYR 0.019 0.002 TYR A 180 PHE 0.023 0.002 PHE A 308 TRP 0.015 0.002 TRP A 165 HIS 0.004 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 ( 5913) covalent geometry : angle 0.59887 / 0.31 ( 8085) SS BOND : bond 0.00151 / 0.10 ( 6) SS BOND : angle 1.37851 / 0.89 ( 12) hydrogen bonds : bond 0.05819 / 3.98 ( 334) hydrogen bonds : angle 4.76113 / 3.53 ( 942) link_ALPHA1-3 : bond 0.00599 / 0.32 ( 1) link_ALPHA1-3 : angle 1.23029 / 0.65 ( 3) link_ALPHA1-6 : bond 0.00430 / 0.23 ( 1) link_ALPHA1-6 : angle 2.01480 / 1.10 ( 3) link_BETA1-4 : bond 0.00366 / 0.19 ( 5) link_BETA1-4 : angle 1.79729 / 1.34 ( 15) link_NAG-ASN : bond 0.00324 / 0.22 ( 8) link_NAG-ASN : angle 2.66684 / 2.01 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8345 (t-100) cc_final: 0.7849 (t-100) REVERT: A 68 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8587 (m) REVERT: A 207 TYR cc_start: 0.8541 (m-80) cc_final: 0.7820 (m-80) REVERT: A 474 MET cc_start: 0.7711 (tpp) cc_final: 0.7370 (mmp) REVERT: A 512 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: B 474 ASN cc_start: 0.7871 (t0) cc_final: 0.7575 (t0) REVERT: B 500 TYR cc_start: 0.5827 (m-80) cc_final: 0.5542 (m-80) outliers start: 9 outliers final: 5 residues processed: 78 average time/residue: 0.0793 time to fit residues: 8.3045 Evaluate side-chains 77 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 459 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.093644 restraints weight = 12725.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.095694 restraints weight = 6430.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.097042 restraints weight = 3928.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.097845 restraints weight = 2733.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.098453 restraints weight = 2138.675| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5934 Z= 0.125 Angle : 0.555 10.170 8142 Z= 0.274 Chirality : 0.042 0.350 901 Planarity : 0.004 0.033 1047 Dihedral : 3.733 15.464 847 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.49 % Allowed : 12.66 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.31), residues: 777 helix: 2.08 (0.26), residues: 413 sheet: 0.32 (0.70), residues: 55 loop : -0.48 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.014 0.001 TYR B 550 PHE 0.011 0.001 PHE A 525 TRP 0.021 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 5913) covalent geometry : angle 0.53639 / 0.27 ( 8085) SS BOND : bond 0.00148 / 0.08 ( 6) SS BOND : angle 0.93836 / 0.65 ( 12) hydrogen bonds : bond 0.04929 / 3.36 ( 334) hydrogen bonds : angle 4.44985 / 3.31 ( 942) link_ALPHA1-3 : bond 0.00554 / 0.29 ( 1) link_ALPHA1-3 : angle 1.28438 / 0.65 ( 3) link_ALPHA1-6 : bond 0.00716 / 0.38 ( 1) link_ALPHA1-6 : angle 1.61509 / 0.88 ( 3) link_BETA1-4 : bond 0.00373 / 0.21 ( 5) link_BETA1-4 : angle 1.59346 / 1.20 ( 15) link_NAG-ASN : bond 0.00300 / 0.18 ( 8) link_NAG-ASN : angle 2.24316 / 1.74 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8289 (t-100) cc_final: 0.7803 (t-100) REVERT: A 68 SER cc_start: 0.8783 (OUTLIER) cc_final: 0.8515 (m) REVERT: A 192 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7914 (ttm-80) REVERT: A 207 TYR cc_start: 0.8483 (m-80) cc_final: 0.7632 (m-80) REVERT: A 512 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: B 474 ASN cc_start: 0.7832 (t0) cc_final: 0.7569 (t0) REVERT: B 500 TYR cc_start: 0.5588 (m-80) cc_final: 0.5297 (m-80) outliers start: 6 outliers final: 4 residues processed: 76 average time/residue: 0.0840 time to fit residues: 8.3850 Evaluate side-chains 76 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 459 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 4 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 36 optimal weight: 0.1980 chunk 39 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.092760 restraints weight = 12919.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.094797 restraints weight = 6635.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.096145 restraints weight = 4098.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.097023 restraints weight = 2881.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097588 restraints weight = 2224.601| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5934 Z= 0.128 Angle : 0.539 9.428 8142 Z= 0.267 Chirality : 0.043 0.371 901 Planarity : 0.004 0.033 1047 Dihedral : 3.672 15.807 847 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.74 % Allowed : 11.91 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.31), residues: 777 helix: 2.08 (0.26), residues: 413 sheet: 0.48 (0.71), residues: 53 loop : -0.56 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.015 0.001 TYR A 183 PHE 0.011 0.001 PHE A 308 TRP 0.019 0.001 TRP A 163 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 5913) covalent geometry : angle 0.52062 / 0.26 ( 8085) SS BOND : bond 0.00106 / 0.06 ( 6) SS BOND : angle 0.88693 / 0.59 ( 12) hydrogen bonds : bond 0.04830 / 3.30 ( 334) hydrogen bonds : angle 4.42076 / 3.29 ( 942) link_ALPHA1-3 : bond 0.00558 / 0.29 ( 1) link_ALPHA1-3 : angle 1.27309 / 0.65 ( 3) link_ALPHA1-6 : bond 0.00540 / 0.28 ( 1) link_ALPHA1-6 : angle 1.67513 / 0.91 ( 3) link_BETA1-4 : bond 0.00309 / 0.18 ( 5) link_BETA1-4 : angle 1.59108 / 1.21 ( 15) link_NAG-ASN : bond 0.00240 / 0.15 ( 8) link_NAG-ASN : angle 2.21359 / 1.71 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8311 (t-100) cc_final: 0.7817 (t-100) REVERT: A 68 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8510 (m) REVERT: A 207 TYR cc_start: 0.8467 (m-80) cc_final: 0.7632 (m-80) REVERT: A 512 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: B 474 ASN cc_start: 0.7825 (t0) cc_final: 0.7579 (t0) REVERT: B 500 TYR cc_start: 0.5640 (m-80) cc_final: 0.5309 (m-80) outliers start: 7 outliers final: 4 residues processed: 76 average time/residue: 0.0772 time to fit residues: 7.8302 Evaluate side-chains 74 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 459 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 0.0030 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 overall best weight: 0.4768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.108955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.095281 restraints weight = 12917.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097367 restraints weight = 6648.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098698 restraints weight = 4090.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.099597 restraints weight = 2866.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.100125 restraints weight = 2211.652| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5934 Z= 0.106 Angle : 0.526 8.872 8142 Z= 0.262 Chirality : 0.041 0.345 901 Planarity : 0.004 0.035 1047 Dihedral : 3.545 15.291 847 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.49 % Allowed : 12.41 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.31), residues: 777 helix: 2.20 (0.26), residues: 415 sheet: 0.49 (0.71), residues: 53 loop : -0.52 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 192 TYR 0.015 0.001 TYR A 315 PHE 0.032 0.001 PHE A 327 TRP 0.022 0.001 TRP A 163 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 ( 5913) covalent geometry : angle 0.51064 / 0.26 ( 8085) SS BOND : bond 0.00131 / 0.07 ( 6) SS BOND : angle 0.77495 / 0.52 ( 12) hydrogen bonds : bond 0.04386 / 3.00 ( 334) hydrogen bonds : angle 4.25319 / 3.16 ( 942) link_ALPHA1-3 : bond 0.00516 / 0.27 ( 1) link_ALPHA1-3 : angle 1.31493 / 0.66 ( 3) link_ALPHA1-6 : bond 0.00551 / 0.29 ( 1) link_ALPHA1-6 : angle 1.40011 / 0.75 ( 3) link_BETA1-4 : bond 0.00316 / 0.19 ( 5) link_BETA1-4 : angle 1.42487 / 1.09 ( 15) link_NAG-ASN : bond 0.00213 / 0.12 ( 8) link_NAG-ASN : angle 1.98567 / 1.56 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8294 (t-100) cc_final: 0.7815 (t-100) REVERT: A 68 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8453 (m) REVERT: A 207 TYR cc_start: 0.8443 (m-80) cc_final: 0.7680 (m-80) REVERT: A 512 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: B 500 TYR cc_start: 0.5555 (m-80) cc_final: 0.5237 (m-80) outliers start: 6 outliers final: 4 residues processed: 77 average time/residue: 0.0674 time to fit residues: 7.0345 Evaluate side-chains 78 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 459 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.094417 restraints weight = 12706.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096466 restraints weight = 6580.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097792 restraints weight = 4075.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098577 restraints weight = 2857.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099209 restraints weight = 2250.545| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5934 Z= 0.117 Angle : 0.523 8.841 8142 Z= 0.260 Chirality : 0.042 0.336 901 Planarity : 0.004 0.032 1047 Dihedral : 3.520 15.221 847 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.24 % Allowed : 12.90 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.31), residues: 777 helix: 2.18 (0.26), residues: 415 sheet: 0.49 (0.71), residues: 53 loop : -0.52 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 192 TYR 0.015 0.001 TYR A 315 PHE 0.010 0.001 PHE A 327 TRP 0.020 0.001 TRP A 163 HIS 0.005 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 ( 5913) covalent geometry : angle 0.50647 / 0.26 ( 8085) SS BOND : bond 0.00142 / 0.07 ( 6) SS BOND : angle 0.83248 / 0.54 ( 12) hydrogen bonds : bond 0.04479 / 3.05 ( 334) hydrogen bonds : angle 4.30566 / 3.19 ( 942) link_ALPHA1-3 : bond 0.00534 / 0.28 ( 1) link_ALPHA1-3 : angle 1.29540 / 0.66 ( 3) link_ALPHA1-6 : bond 0.00636 / 0.33 ( 1) link_ALPHA1-6 : angle 1.63831 / 0.88 ( 3) link_BETA1-4 : bond 0.00337 / 0.19 ( 5) link_BETA1-4 : angle 1.47822 / 1.13 ( 15) link_NAG-ASN : bond 0.00199 / 0.12 ( 8) link_NAG-ASN : angle 2.06399 / 1.62 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1022.50 seconds wall clock time: 18 minutes 21.62 seconds (1101.62 seconds total)