Starting phenix.real_space_refine on Tue Mar 3 14:09:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpz_32693/03_2026/7wpz_32693.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpz_32693/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wpz_32693/03_2026/7wpz_32693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpz_32693/03_2026/7wpz_32693.map" model { file = "/net/cci-nas-00/data/ceres_data/7wpz_32693/03_2026/7wpz_32693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpz_32693/03_2026/7wpz_32693.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.22, per 1000 atoms: 0.21 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: 0.66 Conformation dependent library (CDL) restraints added in 418.4 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: 0.78 Time building geometry restraints manager: 0.81 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 - 21.29: 3529 21.29 - 42.59: 71 42.59 - 63.88: 14 63.88 - 85.17: 9 85.17 - 106.47: 4 Dihedral angle restraints: 3627 sinusoidal: 1321 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 3624 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: 1.070 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: 0.010 Process input model: 7.040 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 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 : 11.149 106.467 2123 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 covalent geometry : bond 0.01343 ( 5913) covalent geometry : angle 1.40915 ( 8085) SS BOND : bond 0.08177 ( 6) SS BOND : angle 3.64828 ( 12) hydrogen bonds : bond 0.20180 ( 334) hydrogen bonds : angle 6.91116 ( 942) link_ALPHA1-3 : bond 0.07174 ( 1) link_ALPHA1-3 : angle 3.78688 ( 3) link_ALPHA1-6 : bond 0.07594 ( 1) link_ALPHA1-6 : angle 1.62593 ( 3) link_BETA1-4 : bond 0.07650 ( 5) link_BETA1-4 : angle 3.68366 ( 15) link_NAG-ASN : bond 0.06766 ( 8) link_NAG-ASN : angle 7.37181 ( 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 : 0.172 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: 0.0945 time to fit residues: 14.5568 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 : 0.125 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3652 r_free = 0.3652 target = 0.125332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.111388 restraints weight = 12079.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113707 restraints weight = 6235.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.115228 restraints weight = 3776.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.116174 restraints weight = 2584.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116780 restraints weight = 1968.379| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5934 Z= 0.152 Angle : 0.664 10.867 8142 Z= 0.339 Chirality : 0.045 0.208 901 Planarity : 0.005 0.040 1047 Dihedral : 7.142 69.121 1156 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.03 % Favored : 98.84 % Rotamer: Outliers : 1.49 % Allowed : 8.19 % Favored : 90.32 % 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: 1.35 (0.29), residues: 777 helix: 1.44 (0.25), residues: 405 sheet: 1.20 (0.63), residues: 54 loop : 0.25 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 219 TYR 0.026 0.002 TYR A 315 PHE 0.022 0.002 PHE A 592 TRP 0.021 0.002 TRP A 163 HIS 0.012 0.002 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5913) covalent geometry : angle 0.62381 ( 8085) SS BOND : bond 0.00720 ( 6) SS BOND : angle 2.41870 ( 12) hydrogen bonds : bond 0.05718 ( 334) hydrogen bonds : angle 4.86535 ( 942) link_ALPHA1-3 : bond 0.00798 ( 1) link_ALPHA1-3 : angle 3.25511 ( 3) link_ALPHA1-6 : bond 0.00044 ( 1) link_ALPHA1-6 : angle 2.24855 ( 3) link_BETA1-4 : bond 0.00719 ( 5) link_BETA1-4 : angle 2.12995 ( 15) link_NAG-ASN : bond 0.00712 ( 8) link_NAG-ASN : angle 3.26481 ( 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 : 0.168 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6881 (mmm) REVERT: A 591 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8752 (tt) REVERT: B 474 ASN cc_start: 0.7644 (t0) cc_final: 0.7329 (t0) REVERT: B 500 TYR cc_start: 0.5715 (m-80) cc_final: 0.5453 (m-80) outliers start: 6 outliers final: 1 residues processed: 75 average time/residue: 0.0691 time to fit residues: 7.1216 Evaluate side-chains 66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 591 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 13 optimal weight: 0.0050 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.3372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.122846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108406 restraints weight = 12176.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.110780 restraints weight = 6161.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112333 restraints weight = 3717.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.113234 restraints weight = 2563.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113943 restraints weight = 1977.756| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5934 Z= 0.116 Angle : 0.529 6.152 8142 Z= 0.272 Chirality : 0.041 0.164 901 Planarity : 0.004 0.030 1047 Dihedral : 6.412 60.918 1156 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.93 % Favored : 97.94 % Rotamer: Outliers : 1.49 % Allowed : 11.17 % 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: 1.77 (0.30), residues: 777 helix: 2.00 (0.25), residues: 401 sheet: 1.33 (0.63), residues: 53 loop : 0.17 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.017 0.001 TYR A 385 PHE 0.016 0.001 PHE A 73 TRP 0.017 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 5913) covalent geometry : angle 0.50440 ( 8085) SS BOND : bond 0.00768 ( 6) SS BOND : angle 1.04839 ( 12) hydrogen bonds : bond 0.05002 ( 334) hydrogen bonds : angle 4.43955 ( 942) link_ALPHA1-3 : bond 0.01171 ( 1) link_ALPHA1-3 : angle 1.61538 ( 3) link_ALPHA1-6 : bond 0.00331 ( 1) link_ALPHA1-6 : angle 1.83902 ( 3) link_BETA1-4 : bond 0.00600 ( 5) link_BETA1-4 : angle 1.52850 ( 15) link_NAG-ASN : bond 0.00428 ( 8) link_NAG-ASN : angle 2.52122 ( 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: 6 poor density : 70 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6923 (mmm) REVERT: B 474 ASN cc_start: 0.7639 (t0) cc_final: 0.7248 (t0) REVERT: B 500 TYR cc_start: 0.5557 (m-80) cc_final: 0.5279 (m-80) outliers start: 6 outliers final: 3 residues processed: 72 average time/residue: 0.0730 time to fit residues: 7.2754 Evaluate side-chains 70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 75 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.110170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.096386 restraints weight = 12638.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.098363 restraints weight = 6718.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099637 restraints weight = 4220.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100521 restraints weight = 3010.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101034 restraints weight = 2341.323| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5934 Z= 0.193 Angle : 0.632 6.988 8142 Z= 0.322 Chirality : 0.045 0.160 901 Planarity : 0.005 0.043 1047 Dihedral : 6.700 52.445 1156 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.19 % Favored : 97.68 % Rotamer: Outliers : 2.48 % Allowed : 11.66 % 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: 1.41 (0.30), residues: 777 helix: 1.60 (0.24), residues: 415 sheet: 0.77 (0.65), residues: 55 loop : 0.16 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 245 TYR 0.022 0.002 TYR A 385 PHE 0.021 0.002 PHE A 592 TRP 0.018 0.002 TRP A 165 HIS 0.006 0.002 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 5913) covalent geometry : angle 0.60511 ( 8085) SS BOND : bond 0.00129 ( 6) SS BOND : angle 1.25172 ( 12) hydrogen bonds : bond 0.05731 ( 334) hydrogen bonds : angle 4.68012 ( 942) link_ALPHA1-3 : bond 0.01133 ( 1) link_ALPHA1-3 : angle 2.90140 ( 3) link_ALPHA1-6 : bond 0.00273 ( 1) link_ALPHA1-6 : angle 2.09304 ( 3) link_BETA1-4 : bond 0.00391 ( 5) link_BETA1-4 : angle 1.73980 ( 15) link_NAG-ASN : bond 0.00483 ( 8) link_NAG-ASN : angle 2.78997 ( 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 85 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 68 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8500 (m) REVERT: A 207 TYR cc_start: 0.8486 (m-80) cc_final: 0.7574 (m-80) REVERT: A 512 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: B 474 ASN cc_start: 0.7806 (t0) cc_final: 0.7424 (t0) REVERT: B 500 TYR cc_start: 0.5724 (m-80) cc_final: 0.5452 (m-80) outliers start: 10 outliers final: 6 residues processed: 80 average time/residue: 0.0703 time to fit residues: 7.7246 Evaluate side-chains 82 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 24 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.108081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.093963 restraints weight = 12985.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.096063 restraints weight = 6639.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.097443 restraints weight = 4073.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.098379 restraints weight = 2841.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098966 restraints weight = 2181.442| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4709 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= 0.159 Angle : 0.575 5.886 8142 Z= 0.291 Chirality : 0.043 0.165 901 Planarity : 0.004 0.036 1047 Dihedral : 6.534 48.934 1156 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.45 % Favored : 97.43 % Rotamer: Outliers : 2.23 % Allowed : 11.17 % Favored : 86.60 % 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: 1.37 (0.31), residues: 777 helix: 1.75 (0.25), residues: 415 sheet: 0.67 (0.68), residues: 53 loop : -0.14 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 575 TYR 0.018 0.002 TYR A 385 PHE 0.021 0.002 PHE A 592 TRP 0.019 0.001 TRP A 163 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 5913) covalent geometry : angle 0.55374 ( 8085) SS BOND : bond 0.00196 ( 6) SS BOND : angle 0.99231 ( 12) hydrogen bonds : bond 0.05265 ( 334) hydrogen bonds : angle 4.59658 ( 942) link_ALPHA1-3 : bond 0.01066 ( 1) link_ALPHA1-3 : angle 2.36970 ( 3) link_ALPHA1-6 : bond 0.00071 ( 1) link_ALPHA1-6 : angle 1.72315 ( 3) link_BETA1-4 : bond 0.00426 ( 5) link_BETA1-4 : angle 1.77331 ( 15) link_NAG-ASN : bond 0.00339 ( 8) link_NAG-ASN : angle 2.35054 ( 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: 9 poor density : 75 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8507 (m) REVERT: A 201 ASP cc_start: 0.8643 (t70) cc_final: 0.8328 (t0) REVERT: A 207 TYR cc_start: 0.8491 (m-80) cc_final: 0.7653 (m-80) REVERT: A 512 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7681 (m-80) REVERT: A 591 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8726 (tt) REVERT: B 474 ASN cc_start: 0.7804 (t0) cc_final: 0.7436 (t0) REVERT: B 500 TYR cc_start: 0.5670 (m-80) cc_final: 0.5409 (m-80) outliers start: 9 outliers final: 4 residues processed: 79 average time/residue: 0.0772 time to fit residues: 8.2675 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 : 0.177 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 485 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094599 restraints weight = 12716.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.096601 restraints weight = 6671.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097909 restraints weight = 4165.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.098767 restraints weight = 2941.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.099318 restraints weight = 2292.769| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5934 Z= 0.127 Angle : 0.558 11.493 8142 Z= 0.274 Chirality : 0.044 0.422 901 Planarity : 0.004 0.033 1047 Dihedral : 5.993 44.658 1156 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.23 % Allowed : 11.66 % 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: 1.53 (0.31), residues: 777 helix: 2.00 (0.25), residues: 413 sheet: 0.65 (0.67), residues: 53 loop : -0.22 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 192 TYR 0.017 0.001 TYR A 385 PHE 0.010 0.001 PHE A 523 TRP 0.019 0.001 TRP A 163 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 5913) covalent geometry : angle 0.53671 ( 8085) SS BOND : bond 0.00136 ( 6) SS BOND : angle 1.05324 ( 12) hydrogen bonds : bond 0.04923 ( 334) hydrogen bonds : angle 4.45332 ( 942) link_ALPHA1-3 : bond 0.01123 ( 1) link_ALPHA1-3 : angle 2.38132 ( 3) link_ALPHA1-6 : bond 0.00205 ( 1) link_ALPHA1-6 : angle 1.79833 ( 3) link_BETA1-4 : bond 0.00382 ( 5) link_BETA1-4 : angle 1.69436 ( 15) link_NAG-ASN : bond 0.00309 ( 8) link_NAG-ASN : angle 2.27333 ( 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 81 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8233 (t-100) cc_final: 0.7696 (t-100) REVERT: A 68 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8484 (m) REVERT: A 201 ASP cc_start: 0.8526 (t70) cc_final: 0.8256 (t0) REVERT: A 207 TYR cc_start: 0.8455 (m-80) cc_final: 0.7649 (m-80) REVERT: A 512 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: B 474 ASN cc_start: 0.7844 (t0) cc_final: 0.7528 (t0) REVERT: B 500 TYR cc_start: 0.5598 (m-80) cc_final: 0.5353 (m-80) outliers start: 9 outliers final: 3 residues processed: 76 average time/residue: 0.0765 time to fit residues: 7.6769 Evaluate side-chains 74 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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: 9.9990 chunk 63 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.102686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.089204 restraints weight = 13066.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.091079 restraints weight = 6930.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.092299 restraints weight = 4365.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.093059 restraints weight = 3107.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.093609 restraints weight = 2457.715| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5934 Z= 0.232 Angle : 0.678 6.435 8142 Z= 0.341 Chirality : 0.047 0.192 901 Planarity : 0.005 0.045 1047 Dihedral : 7.105 48.570 1156 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.99 % Allowed : 11.17 % Favored : 86.85 % 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: 0.81 (0.30), residues: 777 helix: 1.43 (0.25), residues: 410 sheet: 0.19 (0.70), residues: 54 loop : -0.56 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 245 TYR 0.031 0.002 TYR A 180 PHE 0.025 0.002 PHE A 308 TRP 0.016 0.002 TRP A 165 HIS 0.005 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 5913) covalent geometry : angle 0.64920 ( 8085) SS BOND : bond 0.00185 ( 6) SS BOND : angle 1.28011 ( 12) hydrogen bonds : bond 0.06368 ( 334) hydrogen bonds : angle 4.98399 ( 942) link_ALPHA1-3 : bond 0.01028 ( 1) link_ALPHA1-3 : angle 2.64505 ( 3) link_ALPHA1-6 : bond 0.00132 ( 1) link_ALPHA1-6 : angle 2.02780 ( 3) link_BETA1-4 : bond 0.00445 ( 5) link_BETA1-4 : angle 2.11739 ( 15) link_NAG-ASN : bond 0.00410 ( 8) link_NAG-ASN : angle 2.95822 ( 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 81 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8344 (t-100) cc_final: 0.7864 (t-100) REVERT: A 68 SER cc_start: 0.8920 (OUTLIER) cc_final: 0.8651 (m) REVERT: A 201 ASP cc_start: 0.8710 (t70) cc_final: 0.8443 (t0) REVERT: A 207 TYR cc_start: 0.8560 (m-80) cc_final: 0.8059 (m-80) REVERT: A 512 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: B 474 ASN cc_start: 0.7944 (t0) cc_final: 0.7597 (t0) REVERT: B 500 TYR cc_start: 0.5978 (m-80) cc_final: 0.5638 (m-80) outliers start: 8 outliers final: 4 residues processed: 78 average time/residue: 0.0794 time to fit residues: 8.3011 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 : 0.201 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 32 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 0.0070 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.093020 restraints weight = 12951.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.095124 restraints weight = 6610.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.096488 restraints weight = 4037.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.097336 restraints weight = 2798.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097923 restraints weight = 2161.224| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5449 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= 0.124 Angle : 0.552 5.944 8142 Z= 0.274 Chirality : 0.042 0.161 901 Planarity : 0.004 0.035 1047 Dihedral : 6.210 44.926 1156 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.74 % Allowed : 12.16 % 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: 1.21 (0.31), residues: 777 helix: 1.90 (0.26), residues: 413 sheet: 0.05 (0.68), residues: 55 loop : -0.54 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.016 0.001 TYR A 385 PHE 0.012 0.001 PHE A 592 TRP 0.022 0.001 TRP A 163 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5913) covalent geometry : angle 0.52857 ( 8085) SS BOND : bond 0.00112 ( 6) SS BOND : angle 0.90390 ( 12) hydrogen bonds : bond 0.05079 ( 334) hydrogen bonds : angle 4.53792 ( 942) link_ALPHA1-3 : bond 0.01052 ( 1) link_ALPHA1-3 : angle 2.31866 ( 3) link_ALPHA1-6 : bond 0.00297 ( 1) link_ALPHA1-6 : angle 1.73405 ( 3) link_BETA1-4 : bond 0.00416 ( 5) link_BETA1-4 : angle 1.92438 ( 15) link_NAG-ASN : bond 0.00335 ( 8) link_NAG-ASN : angle 2.36015 ( 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: 7 poor density : 71 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8296 (t-100) cc_final: 0.7816 (t-100) REVERT: A 68 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8540 (m) REVERT: A 201 ASP cc_start: 0.8594 (t70) cc_final: 0.8301 (t0) REVERT: A 207 TYR cc_start: 0.8498 (m-80) cc_final: 0.7680 (m-80) REVERT: A 512 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7629 (m-80) REVERT: B 474 ASN cc_start: 0.7859 (t0) cc_final: 0.7558 (t0) REVERT: B 500 TYR cc_start: 0.5648 (m-80) cc_final: 0.5328 (m-80) outliers start: 7 outliers final: 4 residues processed: 74 average time/residue: 0.0803 time to fit residues: 7.9347 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 : 0.215 ------------------------------------------------------------------------------- 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 512 PHE Chi-restraints excluded: chain A residue 524 GLN 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: 5.9990 chunk 50 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 0.0870 chunk 22 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.108234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.094553 restraints weight = 12898.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.096544 restraints weight = 6822.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.097853 restraints weight = 4284.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.098716 restraints weight = 3039.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.099233 restraints weight = 2357.299| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5934 Z= 0.110 Angle : 0.531 10.183 8142 Z= 0.260 Chirality : 0.043 0.335 901 Planarity : 0.004 0.032 1047 Dihedral : 5.534 39.760 1156 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: 1.40 (0.31), residues: 777 helix: 2.10 (0.26), residues: 413 sheet: -0.04 (0.67), residues: 55 loop : -0.49 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 192 TYR 0.016 0.001 TYR A 385 PHE 0.014 0.001 PHE A 592 TRP 0.022 0.001 TRP A 163 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 5913) covalent geometry : angle 0.51109 ( 8085) SS BOND : bond 0.00293 ( 6) SS BOND : angle 0.84229 ( 12) hydrogen bonds : bond 0.04581 ( 334) hydrogen bonds : angle 4.38602 ( 942) link_ALPHA1-3 : bond 0.01190 ( 1) link_ALPHA1-3 : angle 2.15828 ( 3) link_ALPHA1-6 : bond 0.00418 ( 1) link_ALPHA1-6 : angle 1.58160 ( 3) link_BETA1-4 : bond 0.00394 ( 5) link_BETA1-4 : angle 1.72675 ( 15) link_NAG-ASN : bond 0.00278 ( 8) link_NAG-ASN : angle 2.15697 ( 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 75 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8292 (t-100) cc_final: 0.7820 (t-100) REVERT: A 201 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8320 (t0) REVERT: A 207 TYR cc_start: 0.8458 (m-80) cc_final: 0.7649 (m-80) REVERT: A 512 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: B 474 ASN cc_start: 0.7819 (t0) cc_final: 0.7561 (t0) REVERT: B 500 TYR cc_start: 0.5576 (m-80) cc_final: 0.5243 (m-80) outliers start: 6 outliers final: 3 residues processed: 72 average time/residue: 0.0674 time to fit residues: 6.6761 Evaluate side-chains 73 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 201 ASP 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: 0.5980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.107796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.094018 restraints weight = 12918.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.096022 restraints weight = 6754.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.097326 restraints weight = 4220.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.098196 restraints weight = 2989.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098787 restraints weight = 2319.603| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5640 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= 0.115 Angle : 0.538 10.129 8142 Z= 0.263 Chirality : 0.042 0.287 901 Planarity : 0.004 0.034 1047 Dihedral : 5.271 36.728 1156 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.99 % Allowed : 13.15 % 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: 1.47 (0.31), residues: 777 helix: 2.15 (0.26), residues: 415 sheet: 0.22 (0.68), residues: 53 loop : -0.53 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.016 0.001 TYR A 385 PHE 0.013 0.001 PHE A 592 TRP 0.022 0.001 TRP A 163 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 5913) covalent geometry : angle 0.51823 ( 8085) SS BOND : bond 0.00137 ( 6) SS BOND : angle 0.83999 ( 12) hydrogen bonds : bond 0.04548 ( 334) hydrogen bonds : angle 4.34715 ( 942) link_ALPHA1-3 : bond 0.01122 ( 1) link_ALPHA1-3 : angle 2.18566 ( 3) link_ALPHA1-6 : bond 0.00416 ( 1) link_ALPHA1-6 : angle 1.59054 ( 3) link_BETA1-4 : bond 0.00362 ( 5) link_BETA1-4 : angle 1.67238 ( 15) link_NAG-ASN : bond 0.00264 ( 8) link_NAG-ASN : angle 2.17762 ( 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: 4 poor density : 75 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8285 (t-100) cc_final: 0.7794 (t-100) REVERT: A 201 ASP cc_start: 0.8567 (t70) cc_final: 0.8302 (t0) REVERT: A 207 TYR cc_start: 0.8448 (m-80) cc_final: 0.7658 (m-80) REVERT: A 512 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: B 474 ASN cc_start: 0.7815 (t0) cc_final: 0.7584 (t0) REVERT: B 500 TYR cc_start: 0.5628 (m-80) cc_final: 0.5275 (m-80) outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 0.0832 time to fit residues: 8.4612 Evaluate side-chains 76 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET 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: 2.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.105904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.092070 restraints weight = 12810.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.094086 restraints weight = 6713.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095374 restraints weight = 4199.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.096270 restraints weight = 2985.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096871 restraints weight = 2316.824| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5934 Z= 0.144 Angle : 0.564 9.969 8142 Z= 0.278 Chirality : 0.043 0.278 901 Planarity : 0.004 0.035 1047 Dihedral : 5.459 36.319 1156 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.99 % Allowed : 12.66 % 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: 1.28 (0.31), residues: 777 helix: 2.04 (0.26), residues: 415 sheet: 0.13 (0.69), residues: 53 loop : -0.67 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 192 TYR 0.017 0.002 TYR A 385 PHE 0.022 0.002 PHE A 327 TRP 0.018 0.001 TRP A 163 HIS 0.005 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 5913) covalent geometry : angle 0.54238 ( 8085) SS BOND : bond 0.00143 ( 6) SS BOND : angle 0.92311 ( 12) hydrogen bonds : bond 0.04868 ( 334) hydrogen bonds : angle 4.43805 ( 942) link_ALPHA1-3 : bond 0.01084 ( 1) link_ALPHA1-3 : angle 2.34302 ( 3) link_ALPHA1-6 : bond 0.00304 ( 1) link_ALPHA1-6 : angle 1.73240 ( 3) link_BETA1-4 : bond 0.00357 ( 5) link_BETA1-4 : angle 1.75871 ( 15) link_NAG-ASN : bond 0.00230 ( 8) link_NAG-ASN : angle 2.32312 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 953.73 seconds wall clock time: 17 minutes 3.79 seconds (1023.79 seconds total)