Starting phenix.real_space_refine on Thu Jul 24 23:19:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v87_31792/07_2025/7v87_31792.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v87_31792/07_2025/7v87_31792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v87_31792/07_2025/7v87_31792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v87_31792/07_2025/7v87_31792.map" model { file = "/net/cci-nas-00/data/ceres_data/7v87_31792/07_2025/7v87_31792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v87_31792/07_2025/7v87_31792.cif" } resolution = 3.3 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= -0.001 sd= 0.032 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 37 5.16 5 C 4222 2.51 5 N 1085 2.21 5 O 1273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6617 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1593 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.65, per 1000 atoms: 0.85 Number of scatterers: 6617 At special positions: 0 Unit cell: (77, 100.1, 126.5, 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 37 16.00 O 1273 8.00 N 1085 7.00 C 4222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG B 1 " - " ASN A 343 " " NAG C 1 " - " ASN F 90 " " NAG D 1 " - " ASN F 546 " " NAG F2001 " - " ASN F 53 " " NAG F2002 " - " ASN F 103 " " NAG F2003 " - " ASN F 322 " " NAG F2004 " - " ASN F 432 " Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.0 seconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 52.2% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.513A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.820A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.604A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.740A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 80 removed outlier: 3.644A pdb=" N VAL F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TRP F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER F 70 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 101 removed outlier: 3.811A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 154 Processing helix chain 'F' and resid 157 through 171 Processing helix chain 'F' and resid 175 through 194 removed outlier: 4.409A pdb=" N LEU F 179 " --> pdb=" O GLN F 175 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.635A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 231 removed outlier: 3.701A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 251 Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.687A pdb=" N SER F 331 " --> pdb=" O PHE F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.878A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.673A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 412 removed outlier: 3.563A pdb=" N ALA F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.750A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 473 through 485 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 532 removed outlier: 3.502A pdb=" N THR F 517 " --> pdb=" O ILE F 513 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.680A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 588 removed outlier: 3.598A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.885A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.024A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'F' and resid 347 through 350 281 hydrogen bonds defined for protein. 786 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: 2.12 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2104 1.35 - 1.47: 1807 1.47 - 1.59: 2830 1.59 - 1.72: 0 1.72 - 1.84: 58 Bond restraints: 6799 Sorted by residual: bond pdb=" C1 NAG F2004 " pdb=" O5 NAG F2004 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.97e+00 bond pdb=" C1 NAG F2002 " pdb=" O5 NAG F2002 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.98e+00 ... (remaining 6794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 9097 2.31 - 4.63: 118 4.63 - 6.94: 22 6.94 - 9.26: 1 9.26 - 11.57: 1 Bond angle restraints: 9239 Sorted by residual: angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 125.97 -11.57 2.30e+00 1.89e-01 2.53e+01 angle pdb=" N GLU F 479 " pdb=" CA GLU F 479 " pdb=" CB GLU F 479 " ideal model delta sigma weight residual 110.28 116.35 -6.07 1.55e+00 4.16e-01 1.54e+01 angle pdb=" C TRP F 478 " pdb=" N GLU F 479 " pdb=" CA GLU F 479 " ideal model delta sigma weight residual 120.31 114.58 5.73 1.52e+00 4.33e-01 1.42e+01 angle pdb=" N ASN F 90 " pdb=" CA ASN F 90 " pdb=" CB ASN F 90 " ideal model delta sigma weight residual 114.17 110.09 4.08 1.14e+00 7.69e-01 1.28e+01 angle pdb=" C THR F 334 " pdb=" N ASP F 335 " pdb=" CA ASP F 335 " ideal model delta sigma weight residual 121.80 129.82 -8.02 2.44e+00 1.68e-01 1.08e+01 ... (remaining 9234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 3812 21.79 - 43.59: 288 43.59 - 65.38: 44 65.38 - 87.17: 18 87.17 - 108.97: 10 Dihedral angle restraints: 4172 sinusoidal: 1834 harmonic: 2338 Sorted by residual: dihedral pdb=" CA PRO F 146 " pdb=" C PRO F 146 " pdb=" N GLY F 147 " pdb=" CA GLY F 147 " ideal model delta harmonic sigma weight residual -180.00 -154.74 -25.26 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA CYS A 379 " pdb=" C CYS A 379 " pdb=" N TYR A 380 " pdb=" CA TYR A 380 " ideal model delta harmonic sigma weight residual 180.00 -156.24 -23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA PHE A 377 " pdb=" C PHE A 377 " pdb=" N LYS A 378 " pdb=" CA LYS A 378 " ideal model delta harmonic sigma weight residual 180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 4169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 813 0.055 - 0.109: 166 0.109 - 0.164: 15 0.164 - 0.218: 4 0.218 - 0.273: 4 Chirality restraints: 1002 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C1 NAG F2002 " pdb=" ND2 ASN F 103 " pdb=" C2 NAG F2002 " pdb=" O5 NAG F2002 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 999 not shown) Planarity restraints: 1188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO A 521 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 582 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO F 583 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO F 583 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 583 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 89 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.60e+00 pdb=" C GLN F 89 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN F 89 " 0.008 2.00e-02 2.50e+03 pdb=" N ASN F 90 " 0.008 2.00e-02 2.50e+03 ... (remaining 1185 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 196 2.71 - 3.26: 6592 3.26 - 3.81: 10294 3.81 - 4.35: 12193 4.35 - 4.90: 21047 Nonbonded interactions: 50322 Sorted by model distance: nonbonded pdb=" O LEU F 156 " pdb=" OH TYR F 252 " model vdw 2.167 3.040 nonbonded pdb=" NH1 ARG F 161 " pdb=" O HIS F 265 " model vdw 2.244 3.120 nonbonded pdb=" O SER F 77 " pdb=" NE2 GLN F 81 " model vdw 2.283 3.120 nonbonded pdb=" OG SER F 170 " pdb=" OE1 GLU F 171 " model vdw 2.302 3.040 nonbonded pdb=" NZ LYS A 529 " pdb=" O SER A 530 " model vdw 2.304 3.120 ... (remaining 50317 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 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.530 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.003 0.036 6818 Z= 0.167 Angle : 0.669 11.570 9289 Z= 0.348 Chirality : 0.046 0.273 1002 Planarity : 0.004 0.036 1181 Dihedral : 16.491 108.968 2651 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.21 (0.30), residues: 793 helix: 1.12 (0.28), residues: 375 sheet: 0.05 (0.79), residues: 42 loop : -1.51 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 477 HIS 0.005 0.001 HIS F 374 PHE 0.013 0.001 PHE A 347 TYR 0.015 0.001 TYR A 380 ARG 0.002 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00646 ( 7) link_NAG-ASN : angle 3.25487 ( 21) link_BETA1-4 : bond 0.00583 ( 5) link_BETA1-4 : angle 1.51426 ( 15) hydrogen bonds : bond 0.14612 ( 281) hydrogen bonds : angle 5.39246 ( 786) SS BOND : bond 0.00665 ( 7) SS BOND : angle 1.86885 ( 14) covalent geometry : bond 0.00342 ( 6799) covalent geometry : angle 0.64590 ( 9239) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: F 249 MET cc_start: 0.7919 (tpt) cc_final: 0.7684 (mmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2158 time to fit residues: 16.4262 Evaluate side-chains 43 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 0.0060 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 340 GLN ** 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 = 0.3243 r_free = 0.3243 target = 0.062489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.053128 restraints weight = 24082.926| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.39 r_work: 0.2888 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6818 Z= 0.186 Angle : 0.628 10.233 9289 Z= 0.319 Chirality : 0.045 0.280 1002 Planarity : 0.004 0.041 1181 Dihedral : 10.618 72.263 1114 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.57 % Allowed : 6.43 % Favored : 93.00 % 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: -0.15 (0.30), residues: 793 helix: 1.08 (0.28), residues: 384 sheet: 0.11 (0.79), residues: 39 loop : -1.43 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 477 HIS 0.005 0.001 HIS F 493 PHE 0.012 0.001 PHE A 347 TYR 0.015 0.001 TYR F 50 ARG 0.002 0.000 ARG F 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00793 ( 7) link_NAG-ASN : angle 3.05915 ( 21) link_BETA1-4 : bond 0.00560 ( 5) link_BETA1-4 : angle 2.09475 ( 15) hydrogen bonds : bond 0.05242 ( 281) hydrogen bonds : angle 4.48280 ( 786) SS BOND : bond 0.00609 ( 7) SS BOND : angle 1.61332 ( 14) covalent geometry : bond 0.00424 ( 6799) covalent geometry : angle 0.60391 ( 9239) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8561 (m-30) cc_final: 0.8229 (m-30) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.1899 time to fit residues: 11.9833 Evaluate side-chains 43 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 8 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 340 GLN ** 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 = 0.3276 r_free = 0.3276 target = 0.063885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.054584 restraints weight = 23970.975| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.39 r_work: 0.2930 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6818 Z= 0.107 Angle : 0.568 10.346 9289 Z= 0.282 Chirality : 0.042 0.261 1002 Planarity : 0.003 0.039 1181 Dihedral : 7.679 55.034 1114 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.14 % Allowed : 8.86 % Favored : 90.00 % 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: -0.06 (0.30), residues: 793 helix: 1.17 (0.28), residues: 377 sheet: 0.16 (0.79), residues: 42 loop : -1.37 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 477 HIS 0.004 0.001 HIS F 493 PHE 0.011 0.001 PHE F 72 TYR 0.014 0.001 TYR F 50 ARG 0.002 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00724 ( 7) link_NAG-ASN : angle 2.97514 ( 21) link_BETA1-4 : bond 0.00549 ( 5) link_BETA1-4 : angle 2.10549 ( 15) hydrogen bonds : bond 0.04080 ( 281) hydrogen bonds : angle 4.34365 ( 786) SS BOND : bond 0.00360 ( 7) SS BOND : angle 1.21411 ( 14) covalent geometry : bond 0.00232 ( 6799) covalent geometry : angle 0.54273 ( 9239) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: F 323 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7610 (tpp) REVERT: F 479 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8565 (pm20) outliers start: 8 outliers final: 2 residues processed: 48 average time/residue: 0.1824 time to fit residues: 12.5065 Evaluate side-chains 44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 60 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 51 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.065424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.056350 restraints weight = 24814.028| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.34 r_work: 0.2942 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 6818 Z= 0.109 Angle : 0.557 10.336 9289 Z= 0.278 Chirality : 0.042 0.267 1002 Planarity : 0.003 0.040 1181 Dihedral : 6.389 55.089 1114 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.29 % Allowed : 11.00 % Favored : 87.71 % 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: -0.03 (0.30), residues: 793 helix: 1.21 (0.28), residues: 377 sheet: 0.14 (0.78), residues: 42 loop : -1.35 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 477 HIS 0.004 0.001 HIS F 493 PHE 0.012 0.001 PHE F 72 TYR 0.012 0.001 TYR F 50 ARG 0.002 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00709 ( 7) link_NAG-ASN : angle 2.93077 ( 21) link_BETA1-4 : bond 0.00575 ( 5) link_BETA1-4 : angle 2.01182 ( 15) hydrogen bonds : bond 0.03907 ( 281) hydrogen bonds : angle 4.20533 ( 786) SS BOND : bond 0.00448 ( 7) SS BOND : angle 1.35690 ( 14) covalent geometry : bond 0.00244 ( 6799) covalent geometry : angle 0.53150 ( 9239) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 323 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7550 (tpp) REVERT: F 455 MET cc_start: 0.8831 (tmm) cc_final: 0.8505 (tmm) outliers start: 9 outliers final: 5 residues processed: 51 average time/residue: 0.1944 time to fit residues: 13.7851 Evaluate side-chains 48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 468 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 0.0370 chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.063549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.054046 restraints weight = 24193.846| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.47 r_work: 0.2916 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6818 Z= 0.121 Angle : 0.556 10.255 9289 Z= 0.278 Chirality : 0.042 0.270 1002 Planarity : 0.003 0.041 1181 Dihedral : 6.018 55.743 1114 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.43 % Allowed : 11.86 % Favored : 86.71 % 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: 0.03 (0.30), residues: 793 helix: 1.25 (0.28), residues: 377 sheet: 0.45 (0.81), residues: 39 loop : -1.35 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 477 HIS 0.004 0.001 HIS F 493 PHE 0.012 0.001 PHE F 72 TYR 0.012 0.001 TYR F 50 ARG 0.002 0.000 ARG F 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00703 ( 7) link_NAG-ASN : angle 2.90952 ( 21) link_BETA1-4 : bond 0.00548 ( 5) link_BETA1-4 : angle 1.78383 ( 15) hydrogen bonds : bond 0.03984 ( 281) hydrogen bonds : angle 4.16913 ( 786) SS BOND : bond 0.00426 ( 7) SS BOND : angle 1.28694 ( 14) covalent geometry : bond 0.00274 ( 6799) covalent geometry : angle 0.53307 ( 9239) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 323 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7623 (tpp) REVERT: F 455 MET cc_start: 0.8876 (tmm) cc_final: 0.8555 (tmm) REVERT: F 479 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8287 (pm20) outliers start: 10 outliers final: 6 residues processed: 48 average time/residue: 0.1843 time to fit residues: 12.7013 Evaluate side-chains 49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.061711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.052208 restraints weight = 24253.132| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.42 r_work: 0.2864 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6818 Z= 0.191 Angle : 0.604 10.189 9289 Z= 0.307 Chirality : 0.044 0.274 1002 Planarity : 0.004 0.045 1181 Dihedral : 6.234 57.820 1114 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.86 % Allowed : 13.00 % Favored : 85.14 % 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: -0.10 (0.30), residues: 793 helix: 1.15 (0.28), residues: 382 sheet: 0.56 (0.79), residues: 39 loop : -1.49 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 165 HIS 0.004 0.001 HIS F 374 PHE 0.013 0.001 PHE A 347 TYR 0.012 0.001 TYR A 453 ARG 0.002 0.000 ARG F 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00751 ( 7) link_NAG-ASN : angle 2.96831 ( 21) link_BETA1-4 : bond 0.00487 ( 5) link_BETA1-4 : angle 1.78750 ( 15) hydrogen bonds : bond 0.04991 ( 281) hydrogen bonds : angle 4.26965 ( 786) SS BOND : bond 0.00480 ( 7) SS BOND : angle 1.44847 ( 14) covalent geometry : bond 0.00442 ( 6799) covalent geometry : angle 0.58197 ( 9239) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: F 323 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7884 (tpp) REVERT: F 365 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8436 (p) REVERT: F 455 MET cc_start: 0.8965 (tmm) cc_final: 0.8658 (tmm) REVERT: F 479 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8289 (pm20) outliers start: 13 outliers final: 7 residues processed: 51 average time/residue: 0.1863 time to fit residues: 13.4822 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 15 optimal weight: 0.0970 chunk 65 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.062959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.053430 restraints weight = 24140.160| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.47 r_work: 0.2899 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6818 Z= 0.118 Angle : 0.564 10.272 9289 Z= 0.283 Chirality : 0.042 0.260 1002 Planarity : 0.004 0.042 1181 Dihedral : 6.022 56.100 1114 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.86 % Allowed : 14.00 % Favored : 84.14 % 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: 0.06 (0.30), residues: 793 helix: 1.32 (0.28), residues: 376 sheet: 0.75 (0.79), residues: 39 loop : -1.42 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 PHE 0.013 0.001 PHE F 72 TYR 0.011 0.001 TYR F 50 ARG 0.001 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00725 ( 7) link_NAG-ASN : angle 2.93077 ( 21) link_BETA1-4 : bond 0.00480 ( 5) link_BETA1-4 : angle 1.61183 ( 15) hydrogen bonds : bond 0.04083 ( 281) hydrogen bonds : angle 4.17464 ( 786) SS BOND : bond 0.00423 ( 7) SS BOND : angle 1.17059 ( 14) covalent geometry : bond 0.00264 ( 6799) covalent geometry : angle 0.54221 ( 9239) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: F 323 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7830 (tpp) REVERT: F 365 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8427 (p) REVERT: F 455 MET cc_start: 0.8912 (tmm) cc_final: 0.8563 (tmm) REVERT: F 479 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8236 (pm20) outliers start: 13 outliers final: 7 residues processed: 52 average time/residue: 0.1806 time to fit residues: 13.4549 Evaluate side-chains 50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3229 r_free = 0.3229 target = 0.061914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.052402 restraints weight = 24275.506| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.42 r_work: 0.2869 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6818 Z= 0.174 Angle : 0.604 10.233 9289 Z= 0.303 Chirality : 0.044 0.270 1002 Planarity : 0.004 0.045 1181 Dihedral : 6.168 57.161 1114 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.14 % Allowed : 14.29 % Favored : 83.57 % 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: -0.01 (0.30), residues: 793 helix: 1.23 (0.28), residues: 383 sheet: 0.95 (0.80), residues: 39 loop : -1.51 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 165 HIS 0.003 0.001 HIS F 374 PHE 0.011 0.001 PHE F 72 TYR 0.011 0.001 TYR F 50 ARG 0.002 0.000 ARG F 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00733 ( 7) link_NAG-ASN : angle 2.95726 ( 21) link_BETA1-4 : bond 0.00566 ( 5) link_BETA1-4 : angle 1.66921 ( 15) hydrogen bonds : bond 0.04676 ( 281) hydrogen bonds : angle 4.20087 ( 786) SS BOND : bond 0.00434 ( 7) SS BOND : angle 1.38072 ( 14) covalent geometry : bond 0.00401 ( 6799) covalent geometry : angle 0.58260 ( 9239) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: F 323 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7980 (tpp) REVERT: F 365 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8495 (p) REVERT: F 455 MET cc_start: 0.8967 (tmm) cc_final: 0.8619 (tmm) REVERT: F 479 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8279 (pm20) outliers start: 15 outliers final: 8 residues processed: 54 average time/residue: 0.1763 time to fit residues: 14.0368 Evaluate side-chains 52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.0970 chunk 11 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.0570 chunk 59 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.064052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.054588 restraints weight = 24300.925| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.47 r_work: 0.2928 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6818 Z= 0.099 Angle : 0.563 10.359 9289 Z= 0.277 Chirality : 0.042 0.259 1002 Planarity : 0.003 0.039 1181 Dihedral : 5.910 54.877 1114 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.86 % Allowed : 14.57 % Favored : 83.57 % 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: 0.18 (0.30), residues: 793 helix: 1.43 (0.28), residues: 375 sheet: 0.84 (0.80), residues: 42 loop : -1.38 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 477 HIS 0.004 0.001 HIS F 493 PHE 0.013 0.001 PHE F 72 TYR 0.011 0.001 TYR F 50 ARG 0.002 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00712 ( 7) link_NAG-ASN : angle 2.92350 ( 21) link_BETA1-4 : bond 0.00532 ( 5) link_BETA1-4 : angle 1.47892 ( 15) hydrogen bonds : bond 0.03679 ( 281) hydrogen bonds : angle 4.12558 ( 786) SS BOND : bond 0.00412 ( 7) SS BOND : angle 1.08899 ( 14) covalent geometry : bond 0.00212 ( 6799) covalent geometry : angle 0.54258 ( 9239) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: F 227 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8142 (pm20) REVERT: F 323 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7691 (tpp) REVERT: F 455 MET cc_start: 0.8887 (tmm) cc_final: 0.8498 (tmm) REVERT: F 479 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8225 (pm20) outliers start: 13 outliers final: 7 residues processed: 50 average time/residue: 0.1751 time to fit residues: 12.7636 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 77 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 0.0060 chunk 74 optimal weight: 0.0030 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5406 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.064054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.054542 restraints weight = 24565.919| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.48 r_work: 0.2927 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6818 Z= 0.103 Angle : 0.556 10.296 9289 Z= 0.274 Chirality : 0.042 0.266 1002 Planarity : 0.003 0.041 1181 Dihedral : 5.835 55.070 1114 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.57 % Allowed : 15.29 % Favored : 83.14 % 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: 0.26 (0.30), residues: 793 helix: 1.50 (0.28), residues: 376 sheet: 1.09 (0.83), residues: 39 loop : -1.36 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 PHE 0.013 0.001 PHE F 72 TYR 0.012 0.001 TYR F 50 ARG 0.002 0.000 ARG F 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 7) link_NAG-ASN : angle 2.91639 ( 21) link_BETA1-4 : bond 0.00517 ( 5) link_BETA1-4 : angle 1.47935 ( 15) hydrogen bonds : bond 0.03686 ( 281) hydrogen bonds : angle 4.03934 ( 786) SS BOND : bond 0.00377 ( 7) SS BOND : angle 1.10938 ( 14) covalent geometry : bond 0.00226 ( 6799) covalent geometry : angle 0.53521 ( 9239) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: F 323 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7640 (tpp) REVERT: F 365 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8406 (p) REVERT: F 455 MET cc_start: 0.8904 (tmm) cc_final: 0.8502 (tmm) REVERT: F 479 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8220 (pm20) outliers start: 11 outliers final: 7 residues processed: 49 average time/residue: 0.1725 time to fit residues: 12.2760 Evaluate side-chains 51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 13 optimal weight: 0.0980 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.064131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.054614 restraints weight = 24475.724| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.50 r_work: 0.2931 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6818 Z= 0.101 Angle : 0.554 10.268 9289 Z= 0.272 Chirality : 0.041 0.267 1002 Planarity : 0.004 0.040 1181 Dihedral : 5.778 54.962 1114 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.43 % Allowed : 15.43 % Favored : 83.14 % 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: 0.31 (0.31), residues: 793 helix: 1.56 (0.28), residues: 374 sheet: 0.85 (0.82), residues: 42 loop : -1.32 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 PHE 0.013 0.001 PHE F 72 TYR 0.011 0.001 TYR F 50 ARG 0.001 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00684 ( 7) link_NAG-ASN : angle 2.90545 ( 21) link_BETA1-4 : bond 0.00517 ( 5) link_BETA1-4 : angle 1.46419 ( 15) hydrogen bonds : bond 0.03598 ( 281) hydrogen bonds : angle 4.03050 ( 786) SS BOND : bond 0.00370 ( 7) SS BOND : angle 1.08369 ( 14) covalent geometry : bond 0.00223 ( 6799) covalent geometry : angle 0.53303 ( 9239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3411.68 seconds wall clock time: 59 minutes 17.48 seconds (3557.48 seconds total)