Starting phenix.real_space_refine on Thu Jun 5 09:36:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpz_32693/06_2025/7wpz_32693.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpz_32693/06_2025/7wpz_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_32693/06_2025/7wpz_32693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpz_32693/06_2025/7wpz_32693.map" model { file = "/net/cci-nas-00/data/ceres_data/7wpz_32693/06_2025/7wpz_32693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpz_32693/06_2025/7wpz_32693.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 10, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 23, 'GLU:plan': 36} 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: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 8, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 3} 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: 4.79, per 1000 atoms: 0.83 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: 1.89 Conformation dependent library (CDL) restraints added in 936.3 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: 0.84 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: 2.53 Time building geometry restraints manager: 2.07 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 20.430 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.690 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.030 0.005 TRP A 328 HIS 0.005 0.001 HIS A 345 PHE 0.024 0.004 PHE A 592 TYR 0.035 0.005 TYR A 217 ARG 0.006 0.001 ARG A 161 Details of bonding type rmsd link_NAG-ASN : bond 0.06766 ( 8) link_NAG-ASN : angle 7.37181 ( 24) 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_ALPHA1-3 : bond 0.07174 ( 1) link_ALPHA1-3 : angle 3.78688 ( 3) hydrogen bonds : bond 0.20180 ( 334) hydrogen bonds : angle 6.91116 ( 942) SS BOND : bond 0.08177 ( 6) SS BOND : angle 3.64828 ( 12) covalent geometry : bond 0.01343 ( 5913) covalent geometry : angle 1.40915 ( 8085) *********************** 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 : 0.755 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: 0.7319 (mtt) REVERT: A 510 TYR cc_start: 0.6825 (m-80) cc_final: 0.6512 (m-10) REVERT: B 474 ASN cc_start: 0.7697 (t0) cc_final: 0.7387 (t0) REVERT: B 475 GLN cc_start: 0.8105 (tt0) cc_final: 0.7542 (tt0) outliers start: 3 outliers final: 0 residues processed: 123 average time/residue: 0.2544 time to fit residues: 39.5422 Evaluate side-chains 68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.123081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109090 restraints weight = 12038.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.111418 restraints weight = 6191.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112862 restraints weight = 3754.631| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 5934 Z= 0.167 Angle : 0.676 10.396 8142 Z= 0.348 Chirality : 0.045 0.223 901 Planarity : 0.005 0.044 1047 Dihedral : 7.392 73.219 1156 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 0.90 % Favored : 98.97 % Rotamer: Outliers : 1.49 % Allowed : 7.94 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.29), residues: 777 helix: 1.45 (0.25), residues: 405 sheet: 1.22 (0.63), residues: 54 loop : 0.20 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 163 HIS 0.007 0.001 HIS A 345 PHE 0.023 0.002 PHE A 592 TYR 0.027 0.002 TYR A 315 ARG 0.004 0.001 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 8) link_NAG-ASN : angle 3.37574 ( 24) link_ALPHA1-6 : bond 0.00375 ( 1) link_ALPHA1-6 : angle 1.78546 ( 3) link_BETA1-4 : bond 0.00536 ( 5) link_BETA1-4 : angle 2.14746 ( 15) link_ALPHA1-3 : bond 0.00929 ( 1) link_ALPHA1-3 : angle 2.52434 ( 3) hydrogen bonds : bond 0.06354 ( 334) hydrogen bonds : angle 4.94747 ( 942) SS BOND : bond 0.00842 ( 6) SS BOND : angle 2.82785 ( 12) covalent geometry : bond 0.00339 ( 5913) covalent geometry : angle 0.63414 ( 8085) *********************** 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 : 0.716 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6583 (mmm) REVERT: B 474 ASN cc_start: 0.7717 (t0) cc_final: 0.7352 (t0) outliers start: 6 outliers final: 1 residues processed: 76 average time/residue: 0.1658 time to fit residues: 17.4478 Evaluate side-chains 62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 294 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.114919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100825 restraints weight = 12475.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.102959 restraints weight = 6520.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.104345 restraints weight = 4043.401| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5934 Z= 0.146 Angle : 0.570 6.140 8142 Z= 0.296 Chirality : 0.043 0.165 901 Planarity : 0.004 0.037 1047 Dihedral : 6.815 61.422 1156 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.32 % Favored : 97.55 % Rotamer: Outliers : 2.23 % Allowed : 10.17 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.30), residues: 777 helix: 1.78 (0.25), residues: 406 sheet: 1.50 (0.64), residues: 53 loop : -0.02 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 165 HIS 0.003 0.001 HIS B 485 PHE 0.021 0.002 PHE A 592 TYR 0.021 0.002 TYR A 385 ARG 0.003 0.001 ARG A 575 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 8) link_NAG-ASN : angle 2.55434 ( 24) link_ALPHA1-6 : bond 0.00266 ( 1) link_ALPHA1-6 : angle 1.74062 ( 3) link_BETA1-4 : bond 0.00671 ( 5) link_BETA1-4 : angle 1.52203 ( 15) link_ALPHA1-3 : bond 0.01242 ( 1) link_ALPHA1-3 : angle 1.76419 ( 3) hydrogen bonds : bond 0.05419 ( 334) hydrogen bonds : angle 4.58277 ( 942) SS BOND : bond 0.00346 ( 6) SS BOND : angle 1.22623 ( 12) covalent geometry : bond 0.00298 ( 5913) covalent geometry : angle 0.54688 ( 8085) *********************** 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 82 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8209 (t0) REVERT: A 207 TYR cc_start: 0.8419 (m-80) cc_final: 0.7461 (m-80) REVERT: A 512 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: B 474 ASN cc_start: 0.7752 (t0) cc_final: 0.7365 (t0) REVERT: B 500 TYR cc_start: 0.5534 (m-80) cc_final: 0.5241 (m-80) outliers start: 9 outliers final: 6 residues processed: 77 average time/residue: 0.1796 time to fit residues: 19.5000 Evaluate side-chains 78 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 86 LEU 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 B residue 442 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 9 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 0.0470 chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.112284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.098582 restraints weight = 12766.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100652 restraints weight = 6702.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.102029 restraints weight = 4156.024| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5934 Z= 0.129 Angle : 0.544 5.957 8142 Z= 0.272 Chirality : 0.042 0.171 901 Planarity : 0.004 0.035 1047 Dihedral : 5.981 47.957 1156 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.54 % Favored : 98.33 % Rotamer: Outliers : 1.74 % Allowed : 11.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.31), residues: 777 helix: 1.91 (0.25), residues: 413 sheet: 1.18 (0.65), residues: 53 loop : 0.00 (0.38), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.003 0.001 HIS A 373 PHE 0.016 0.001 PHE A 592 TYR 0.018 0.002 TYR B 550 ARG 0.004 0.001 ARG A 575 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 8) link_NAG-ASN : angle 2.32255 ( 24) link_ALPHA1-6 : bond 0.00018 ( 1) link_ALPHA1-6 : angle 1.89449 ( 3) link_BETA1-4 : bond 0.00334 ( 5) link_BETA1-4 : angle 1.66027 ( 15) link_ALPHA1-3 : bond 0.01060 ( 1) link_ALPHA1-3 : angle 2.94068 ( 3) hydrogen bonds : bond 0.04815 ( 334) hydrogen bonds : angle 4.39195 ( 942) SS BOND : bond 0.00138 ( 6) SS BOND : angle 1.40366 ( 12) covalent geometry : bond 0.00263 ( 5913) covalent geometry : angle 0.51871 ( 8085) *********************** 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 : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 SER cc_start: 0.8731 (p) cc_final: 0.8397 (m) REVERT: A 201 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8177 (t0) REVERT: A 207 TYR cc_start: 0.8403 (m-80) cc_final: 0.7488 (m-80) REVERT: A 512 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: B 474 ASN cc_start: 0.7844 (t0) cc_final: 0.7470 (t0) REVERT: B 500 TYR cc_start: 0.5577 (m-80) cc_final: 0.5312 (m-80) outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.2438 time to fit residues: 25.4138 Evaluate side-chains 80 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 73 optimal weight: 0.8980 chunk 68 optimal weight: 0.0040 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 63 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.112474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098385 restraints weight = 12465.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100548 restraints weight = 6353.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.101985 restraints weight = 3893.669| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5934 Z= 0.110 Angle : 0.506 5.607 8142 Z= 0.253 Chirality : 0.041 0.172 901 Planarity : 0.004 0.031 1047 Dihedral : 5.567 43.443 1156 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.49 % Allowed : 12.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.31), residues: 777 helix: 2.06 (0.25), residues: 415 sheet: 1.01 (0.66), residues: 53 loop : -0.00 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.004 0.001 HIS A 373 PHE 0.015 0.001 PHE A 525 TYR 0.016 0.001 TYR A 385 ARG 0.007 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 8) link_NAG-ASN : angle 2.04979 ( 24) link_ALPHA1-6 : bond 0.00045 ( 1) link_ALPHA1-6 : angle 1.71280 ( 3) link_BETA1-4 : bond 0.00413 ( 5) link_BETA1-4 : angle 1.49055 ( 15) link_ALPHA1-3 : bond 0.01202 ( 1) link_ALPHA1-3 : angle 2.18728 ( 3) hydrogen bonds : bond 0.04549 ( 334) hydrogen bonds : angle 4.26756 ( 942) SS BOND : bond 0.00158 ( 6) SS BOND : angle 0.95891 ( 12) covalent geometry : bond 0.00215 ( 5913) covalent geometry : angle 0.48649 ( 8085) *********************** 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 80 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 SER cc_start: 0.8688 (OUTLIER) cc_final: 0.8339 (m) REVERT: A 201 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8181 (t0) REVERT: A 207 TYR cc_start: 0.8386 (m-80) cc_final: 0.7485 (m-80) REVERT: A 512 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: B 474 ASN cc_start: 0.7796 (t0) cc_final: 0.7434 (t0) REVERT: B 500 TYR cc_start: 0.5527 (m-80) cc_final: 0.5262 (m-80) outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 0.2101 time to fit residues: 21.2757 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 : 0.668 ------------------------------------------------------------------------------- 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 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 26 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS A 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.104094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.090171 restraints weight = 12712.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.092171 restraints weight = 6550.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.093433 restraints weight = 4057.414| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5934 Z= 0.232 Angle : 0.656 6.591 8142 Z= 0.331 Chirality : 0.045 0.173 901 Planarity : 0.005 0.044 1047 Dihedral : 6.658 46.166 1156 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.30), residues: 777 helix: 1.60 (0.25), residues: 415 sheet: 0.29 (0.69), residues: 55 loop : -0.33 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 165 HIS 0.005 0.002 HIS A 265 PHE 0.025 0.002 PHE A 308 TYR 0.022 0.002 TYR A 385 ARG 0.015 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 8) link_NAG-ASN : angle 2.87765 ( 24) link_ALPHA1-6 : bond 0.00274 ( 1) link_ALPHA1-6 : angle 2.20043 ( 3) link_BETA1-4 : bond 0.00494 ( 5) link_BETA1-4 : angle 1.95656 ( 15) link_ALPHA1-3 : bond 0.00922 ( 1) link_ALPHA1-3 : angle 2.84105 ( 3) hydrogen bonds : bond 0.06028 ( 334) hydrogen bonds : angle 4.81832 ( 942) SS BOND : bond 0.00434 ( 6) SS BOND : angle 1.26557 ( 12) covalent geometry : bond 0.00511 ( 5913) covalent geometry : angle 0.62841 ( 8085) *********************** 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 84 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8301 (t-100) cc_final: 0.7807 (t-100) REVERT: A 68 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8596 (m) REVERT: A 201 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8404 (t0) REVERT: A 207 TYR cc_start: 0.8529 (m-80) cc_final: 0.7791 (m-80) REVERT: A 512 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7778 (m-80) REVERT: A 591 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9059 (tt) REVERT: B 474 ASN cc_start: 0.7905 (t0) cc_final: 0.7492 (t0) REVERT: B 500 TYR cc_start: 0.5872 (m-80) cc_final: 0.5537 (m-80) outliers start: 10 outliers final: 5 residues processed: 79 average time/residue: 0.1798 time to fit residues: 19.2640 Evaluate side-chains 80 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 201 ASP 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 Chi-restraints excluded: chain B residue 459 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 0.0470 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.108939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.095161 restraints weight = 12695.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.097278 restraints weight = 6490.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.098686 restraints weight = 3974.806| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5934 Z= 0.110 Angle : 0.535 7.612 8142 Z= 0.266 Chirality : 0.042 0.203 901 Planarity : 0.004 0.030 1047 Dihedral : 5.693 41.485 1156 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.23 % Allowed : 12.16 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.31), residues: 777 helix: 2.05 (0.26), residues: 415 sheet: 0.55 (0.67), residues: 53 loop : -0.31 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 163 HIS 0.003 0.000 HIS A 241 PHE 0.010 0.001 PHE A 525 TYR 0.015 0.001 TYR A 385 ARG 0.007 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 8) link_NAG-ASN : angle 2.16769 ( 24) link_ALPHA1-6 : bond 0.00241 ( 1) link_ALPHA1-6 : angle 1.58140 ( 3) link_BETA1-4 : bond 0.00449 ( 5) link_BETA1-4 : angle 1.72624 ( 15) link_ALPHA1-3 : bond 0.01164 ( 1) link_ALPHA1-3 : angle 2.23813 ( 3) hydrogen bonds : bond 0.04692 ( 334) hydrogen bonds : angle 4.36947 ( 942) SS BOND : bond 0.00282 ( 6) SS BOND : angle 0.90424 ( 12) covalent geometry : bond 0.00216 ( 5913) covalent geometry : angle 0.51487 ( 8085) *********************** 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 78 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7655 (pm20) cc_final: 0.7359 (tt0) REVERT: A 49 TRP cc_start: 0.8256 (t-100) cc_final: 0.7714 (t-100) REVERT: A 68 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8478 (m) REVERT: A 201 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8256 (t0) REVERT: A 207 TYR cc_start: 0.8459 (m-80) cc_final: 0.7662 (m-80) REVERT: A 512 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: B 474 ASN cc_start: 0.7845 (t0) cc_final: 0.7484 (t0) REVERT: B 500 TYR cc_start: 0.5580 (m-80) cc_final: 0.5271 (m-80) outliers start: 9 outliers final: 3 residues processed: 74 average time/residue: 0.1676 time to fit residues: 16.6626 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 : 0.596 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.108721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.094976 restraints weight = 12573.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.097096 restraints weight = 6447.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.098482 restraints weight = 3959.908| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5934 Z= 0.117 Angle : 0.524 5.696 8142 Z= 0.261 Chirality : 0.041 0.174 901 Planarity : 0.004 0.031 1047 Dihedral : 5.349 37.970 1156 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.74 % Allowed : 11.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.31), residues: 777 helix: 2.13 (0.26), residues: 415 sheet: 0.25 (0.67), residues: 55 loop : -0.28 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.002 0.001 HIS A 241 PHE 0.013 0.001 PHE A 327 TYR 0.016 0.001 TYR A 385 ARG 0.007 0.001 ARG B 483 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 8) link_NAG-ASN : angle 2.19825 ( 24) link_ALPHA1-6 : bond 0.00342 ( 1) link_ALPHA1-6 : angle 1.63627 ( 3) link_BETA1-4 : bond 0.00381 ( 5) link_BETA1-4 : angle 1.64075 ( 15) link_ALPHA1-3 : bond 0.01178 ( 1) link_ALPHA1-3 : angle 2.30239 ( 3) hydrogen bonds : bond 0.04628 ( 334) hydrogen bonds : angle 4.30828 ( 942) SS BOND : bond 0.00059 ( 6) SS BOND : angle 0.77485 ( 12) covalent geometry : bond 0.00240 ( 5913) covalent geometry : angle 0.50378 ( 8085) *********************** 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 79 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8265 (t-100) cc_final: 0.7673 (t-100) REVERT: A 68 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8455 (m) REVERT: A 201 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8281 (t0) REVERT: A 207 TYR cc_start: 0.8454 (m-80) cc_final: 0.7654 (m-80) REVERT: A 512 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7674 (m-80) REVERT: B 474 ASN cc_start: 0.7868 (t0) cc_final: 0.7525 (t0) REVERT: B 500 TYR cc_start: 0.5639 (m-80) cc_final: 0.5348 (m-80) outliers start: 7 outliers final: 4 residues processed: 76 average time/residue: 0.1658 time to fit residues: 17.1860 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 : 0.590 ------------------------------------------------------------------------------- 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 201 ASP 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 73 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.109129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.095435 restraints weight = 12665.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.097539 restraints weight = 6532.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.098927 restraints weight = 4027.567| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5934 Z= 0.119 Angle : 0.523 5.640 8142 Z= 0.261 Chirality : 0.041 0.174 901 Planarity : 0.004 0.036 1047 Dihedral : 5.193 35.527 1156 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.31), residues: 777 helix: 2.17 (0.26), residues: 415 sheet: 0.30 (0.67), residues: 55 loop : -0.33 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.002 0.001 HIS A 374 PHE 0.015 0.001 PHE A 84 TYR 0.016 0.001 TYR A 385 ARG 0.006 0.001 ARG B 483 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 8) link_NAG-ASN : angle 2.14923 ( 24) link_ALPHA1-6 : bond 0.00293 ( 1) link_ALPHA1-6 : angle 1.58250 ( 3) link_BETA1-4 : bond 0.00370 ( 5) link_BETA1-4 : angle 1.62161 ( 15) link_ALPHA1-3 : bond 0.01380 ( 1) link_ALPHA1-3 : angle 2.45808 ( 3) hydrogen bonds : bond 0.04560 ( 334) hydrogen bonds : angle 4.28220 ( 942) SS BOND : bond 0.00105 ( 6) SS BOND : angle 0.81781 ( 12) covalent geometry : bond 0.00248 ( 5913) covalent geometry : angle 0.50287 ( 8085) *********************** 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 80 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8286 (t-100) cc_final: 0.7697 (t-100) REVERT: A 68 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8443 (m) REVERT: A 201 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8256 (t0) REVERT: A 207 TYR cc_start: 0.8450 (m-80) cc_final: 0.7683 (m-80) REVERT: A 512 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: B 474 ASN cc_start: 0.7866 (t0) cc_final: 0.7514 (t0) REVERT: B 500 TYR cc_start: 0.5616 (m-80) cc_final: 0.5288 (m-80) outliers start: 7 outliers final: 3 residues processed: 77 average time/residue: 0.1873 time to fit residues: 19.2952 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 : 0.673 ------------------------------------------------------------------------------- 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 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 10 optimal weight: 0.7980 chunk 47 optimal weight: 0.0980 chunk 70 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.108065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.094540 restraints weight = 12676.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.096490 restraints weight = 6843.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.097767 restraints weight = 4349.123| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 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 0.041 5934 Z= 0.120 Angle : 0.517 5.679 8142 Z= 0.257 Chirality : 0.041 0.176 901 Planarity : 0.004 0.031 1047 Dihedral : 5.065 33.398 1156 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.49 % Allowed : 11.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.31), residues: 777 helix: 2.20 (0.26), residues: 415 sheet: 0.22 (0.67), residues: 55 loop : -0.41 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.002 0.001 HIS A 241 PHE 0.018 0.001 PHE A 327 TYR 0.016 0.001 TYR A 385 ARG 0.006 0.001 ARG B 483 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 8) link_NAG-ASN : angle 2.18068 ( 24) link_ALPHA1-6 : bond 0.00362 ( 1) link_ALPHA1-6 : angle 1.61497 ( 3) link_BETA1-4 : bond 0.00349 ( 5) link_BETA1-4 : angle 1.60907 ( 15) link_ALPHA1-3 : bond 0.01146 ( 1) link_ALPHA1-3 : angle 2.24885 ( 3) hydrogen bonds : bond 0.04558 ( 334) hydrogen bonds : angle 4.27450 ( 942) SS BOND : bond 0.00127 ( 6) SS BOND : angle 0.83591 ( 12) covalent geometry : bond 0.00250 ( 5913) covalent geometry : angle 0.49651 ( 8085) ********************** 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 80 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 49 TRP cc_start: 0.8310 (t-100) cc_final: 0.7734 (t-100) REVERT: A 68 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8455 (m) REVERT: A 201 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8232 (t0) REVERT: A 207 TYR cc_start: 0.8429 (m-80) cc_final: 0.7672 (m-80) REVERT: A 512 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: B 474 ASN cc_start: 0.7890 (t0) cc_final: 0.7587 (t0) REVERT: B 500 TYR cc_start: 0.5612 (m-80) cc_final: 0.5305 (m-80) REVERT: B 543 PHE cc_start: 0.8329 (m-80) cc_final: 0.8070 (m-80) outliers start: 6 outliers final: 3 residues processed: 77 average time/residue: 0.1860 time to fit residues: 18.8789 Evaluate side-chains 77 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 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 23 optimal weight: 0.6980 chunk 65 optimal weight: 0.0770 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.110345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096582 restraints weight = 12765.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.098694 restraints weight = 6619.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100089 restraints weight = 4099.061| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5934 Z= 0.104 Angle : 0.504 6.637 8142 Z= 0.250 Chirality : 0.040 0.151 901 Planarity : 0.003 0.031 1047 Dihedral : 4.627 30.311 1156 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.99 % Allowed : 12.66 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.31), residues: 777 helix: 2.34 (0.26), residues: 415 sheet: 0.40 (0.68), residues: 53 loop : -0.39 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 163 HIS 0.004 0.001 HIS A 159 PHE 0.012 0.001 PHE A 327 TYR 0.016 0.001 TYR A 385 ARG 0.006 0.001 ARG B 483 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 8) link_NAG-ASN : angle 1.96910 ( 24) link_ALPHA1-6 : bond 0.00522 ( 1) link_ALPHA1-6 : angle 1.47369 ( 3) link_BETA1-4 : bond 0.00391 ( 5) link_BETA1-4 : angle 1.47925 ( 15) link_ALPHA1-3 : bond 0.01160 ( 1) link_ALPHA1-3 : angle 2.00438 ( 3) hydrogen bonds : bond 0.04136 ( 334) hydrogen bonds : angle 4.14068 ( 942) SS BOND : bond 0.00112 ( 6) SS BOND : angle 0.70245 ( 12) covalent geometry : bond 0.00210 ( 5913) covalent geometry : angle 0.48659 ( 8085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2211.81 seconds wall clock time: 39 minutes 55.18 seconds (2395.18 seconds total)