Starting phenix.real_space_refine on Wed Jul 23 23:01:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xpy_38563/07_2025/8xpy_38563.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xpy_38563/07_2025/8xpy_38563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xpy_38563/07_2025/8xpy_38563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xpy_38563/07_2025/8xpy_38563.map" model { file = "/net/cci-nas-00/data/ceres_data/8xpy_38563/07_2025/8xpy_38563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xpy_38563/07_2025/8xpy_38563.cif" } resolution = 3.63 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= -0.024 sd= 0.394 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 25 5.16 5 C 2875 2.51 5 N 730 2.21 5 O 938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 4568 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3365 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 400} Chain: "B" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 898 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 116} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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: "G" 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 Time building chain proxies: 3.20, per 1000 atoms: 0.70 Number of scatterers: 4568 At special positions: 0 Unit cell: (75.492, 81.084, 108.112, 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 25 16.00 O 938 8.00 N 730 7.00 C 2875 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 240 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 503 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 574 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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 ALPHA1-3 " BMA D 3 " - " MAN D 6 " " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " ALPHA1-6 " BMA C 3 " - " MAN C 4 " " MAN C 4 " - " MAN C 5 " " BMA D 3 " - " MAN D 4 " " MAN D 4 " - " MAN D 5 " " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG G 1 " - " ASN A 481 " Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 489.8 milliseconds 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 11 sheets defined 4.6% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... 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 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 391 through 399 removed outlier: 4.267A pdb=" N CYS A 395 " --> pdb=" O PRO A 392 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG A 396 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 397 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 398 " --> pdb=" O CYS A 395 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N MET A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.505A pdb=" N LYS B 65 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.957A pdb=" N THR B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 201 through 202 removed outlier: 3.557A pdb=" N ILE A 580 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 216 through 218 Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 218 removed outlier: 3.507A pdb=" N HIS A 233 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 249 " --> pdb=" O HIS A 233 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 235 " --> pdb=" O GLN A 247 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN A 247 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE A 237 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER A 245 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL A 270 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 252 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 279 through 280 Processing sheet with id=AA5, first strand: chain 'A' and resid 279 through 280 removed outlier: 3.509A pdb=" N LEU A 319 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET A 316 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 340 through 341 removed outlier: 4.264A pdb=" N PHE A 428 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS A 347 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 341 removed outlier: 4.264A pdb=" N PHE A 428 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 442 through 446 removed outlier: 4.324A pdb=" N LYS A 465 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL A 476 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 512 through 515 removed outlier: 7.098A pdb=" N ILE A 520 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 17 through 18 Processing sheet with id=AB2, first strand: chain 'B' and resid 58 through 59 removed outlier: 3.579A pdb=" N ASN B 59 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 48 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 113 " --> pdb=" O TYR B 94 " (cutoff:3.500A) 124 hydrogen bonds defined for protein. 324 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: 1.20 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1398 1.34 - 1.46: 1110 1.46 - 1.58: 2126 1.58 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 4668 Sorted by residual: bond pdb=" C3 BMA D 3 " pdb=" O3 BMA D 3 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.564 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.561 -0.042 2.00e-02 2.50e+03 4.48e+00 bond pdb=" C5 MAN F 5 " pdb=" O5 MAN F 5 " ideal model delta sigma weight residual 1.418 1.460 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C5 MAN D 6 " pdb=" O5 MAN D 6 " ideal model delta sigma weight residual 1.418 1.459 -0.041 2.00e-02 2.50e+03 4.30e+00 ... (remaining 4663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 6103 1.69 - 3.38: 176 3.38 - 5.08: 45 5.08 - 6.77: 23 6.77 - 8.46: 1 Bond angle restraints: 6348 Sorted by residual: angle pdb=" N ALA B 101 " pdb=" CA ALA B 101 " pdb=" C ALA B 101 " ideal model delta sigma weight residual 107.73 111.89 -4.16 1.34e+00 5.57e-01 9.63e+00 angle pdb=" CA LEU A 418 " pdb=" CB LEU A 418 " pdb=" CG LEU A 418 " ideal model delta sigma weight residual 116.30 124.76 -8.46 3.50e+00 8.16e-02 5.84e+00 angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.31 6.64 3.00e+00 1.11e-01 4.90e+00 angle pdb=" C1 BMA F 3 " pdb=" O5 BMA F 3 " pdb=" C5 BMA F 3 " ideal model delta sigma weight residual 118.82 112.42 6.40 3.00e+00 1.11e-01 4.54e+00 angle pdb=" C1 BMA E 3 " pdb=" O5 BMA E 3 " pdb=" C5 BMA E 3 " ideal model delta sigma weight residual 118.82 112.57 6.25 3.00e+00 1.11e-01 4.34e+00 ... (remaining 6343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.80: 2837 25.80 - 51.60: 86 51.60 - 77.40: 44 77.40 - 103.20: 101 103.20 - 129.00: 42 Dihedral angle restraints: 3110 sinusoidal: 1534 harmonic: 1576 Sorted by residual: dihedral pdb=" CA SER B 54 " pdb=" C SER B 54 " pdb=" N SER B 55 " pdb=" CA SER B 55 " ideal model delta harmonic sigma weight residual -180.00 -157.06 -22.94 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" C1 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " pdb=" C6 NAG D 1 " ideal model delta sinusoidal sigma weight residual 171.16 -59.84 -129.00 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C1 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " pdb=" C4 NAG D 1 " ideal model delta sinusoidal sigma weight residual -64.11 64.13 -128.24 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 3107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 629 0.056 - 0.112: 111 0.112 - 0.168: 29 0.168 - 0.225: 1 0.225 - 0.281: 6 Chirality restraints: 776 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 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 -2.54 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 773 not shown) Planarity restraints: 776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 440 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO A 441 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 450 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO A 451 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 382 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO A 383 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 383 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 383 " 0.016 5.00e-02 4.00e+02 ... (remaining 773 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 446 2.75 - 3.29: 4394 3.29 - 3.83: 7570 3.83 - 4.36: 8402 4.36 - 4.90: 14805 Nonbonded interactions: 35617 Sorted by model distance: nonbonded pdb=" OG SER B 7 " pdb=" OG SER B 21 " model vdw 2.217 3.040 nonbonded pdb=" O3 NAG E 2 " pdb=" O3 BMA E 3 " model vdw 2.231 3.040 nonbonded pdb=" O3 NAG F 2 " pdb=" O2 BMA F 3 " model vdw 2.235 3.040 nonbonded pdb=" O PHE B 29 " pdb=" NH2 ARG B 72 " model vdw 2.299 3.120 nonbonded pdb=" OG SER B 35 " pdb=" O GLY B 99 " model vdw 2.299 3.040 ... (remaining 35612 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' } 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: 1.010 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.660 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 : 0.004 0.050 4697 Z= 0.230 Angle : 0.801 8.461 6427 Z= 0.356 Chirality : 0.053 0.281 776 Planarity : 0.004 0.050 775 Dihedral : 29.421 128.998 2082 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 4.39 % Allowed : 6.28 % Favored : 89.33 % 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: -4.21 (0.29), residues: 542 helix: -4.52 (0.53), residues: 12 sheet: -1.82 (0.34), residues: 182 loop : -3.50 (0.26), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 36 HIS 0.000 0.000 HIS A 333 PHE 0.007 0.001 PHE A 466 TYR 0.004 0.001 TYR A 581 ARG 0.002 0.000 ARG A 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 1) link_NAG-ASN : angle 2.56768 ( 3) link_ALPHA1-6 : bond 0.00509 ( 7) link_ALPHA1-6 : angle 1.57968 ( 21) link_BETA1-4 : bond 0.00750 ( 10) link_BETA1-4 : angle 1.48234 ( 30) link_ALPHA1-3 : bond 0.00642 ( 3) link_ALPHA1-3 : angle 2.18136 ( 9) hydrogen bonds : bond 0.16409 ( 103) hydrogen bonds : angle 7.36745 ( 324) SS BOND : bond 0.00067 ( 8) SS BOND : angle 0.47994 ( 16) covalent geometry : bond 0.00447 ( 4668) covalent geometry : angle 0.78734 ( 6348) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLN cc_start: 0.7916 (tt0) cc_final: 0.7687 (tt0) REVERT: A 389 TYR cc_start: 0.6153 (m-10) cc_final: 0.5784 (m-10) REVERT: A 394 ASN cc_start: 0.8019 (m-40) cc_final: 0.7568 (m-40) REVERT: A 573 TRP cc_start: 0.7828 (m100) cc_final: 0.7547 (m100) REVERT: B 25 SER cc_start: 0.8140 (t) cc_final: 0.7898 (t) REVERT: B 68 PHE cc_start: 0.8764 (m-10) cc_final: 0.8093 (m-80) outliers start: 21 outliers final: 6 residues processed: 146 average time/residue: 0.2244 time to fit residues: 38.9103 Evaluate side-chains 91 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 69 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.0970 chunk 13 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 269 ASN A 281 HIS A 333 HIS A 406 HIS A 492 GLN A 509 ASN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.068914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.062424 restraints weight = 16855.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.064031 restraints weight = 7921.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.065044 restraints weight = 4510.451| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4697 Z= 0.160 Angle : 0.910 8.824 6427 Z= 0.392 Chirality : 0.057 0.281 776 Planarity : 0.005 0.047 775 Dihedral : 29.221 114.903 1105 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 3.56 % Allowed : 13.60 % Favored : 82.85 % 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: -3.39 (0.32), residues: 542 helix: -4.26 (0.34), residues: 12 sheet: -1.31 (0.36), residues: 192 loop : -2.90 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 104 HIS 0.003 0.001 HIS A 333 PHE 0.016 0.002 PHE B 27 TYR 0.015 0.002 TYR A 416 ARG 0.009 0.001 ARG A 402 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 1) link_NAG-ASN : angle 1.92253 ( 3) link_ALPHA1-6 : bond 0.01089 ( 7) link_ALPHA1-6 : angle 2.52265 ( 21) link_BETA1-4 : bond 0.00763 ( 10) link_BETA1-4 : angle 2.79042 ( 30) link_ALPHA1-3 : bond 0.00985 ( 3) link_ALPHA1-3 : angle 3.38416 ( 9) hydrogen bonds : bond 0.03519 ( 103) hydrogen bonds : angle 5.47044 ( 324) SS BOND : bond 0.00445 ( 8) SS BOND : angle 1.02417 ( 16) covalent geometry : bond 0.00354 ( 4668) covalent geometry : angle 0.87201 ( 6348) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.7281 (ttm) cc_final: 0.6727 (ttm) REVERT: A 394 ASN cc_start: 0.7976 (m-40) cc_final: 0.7514 (m-40) REVERT: A 463 MET cc_start: 0.8596 (mmt) cc_final: 0.8107 (mmt) REVERT: B 32 TYR cc_start: 0.7337 (m-10) cc_final: 0.6987 (m-80) REVERT: B 57 TYR cc_start: 0.6557 (t80) cc_final: 0.6344 (t80) REVERT: B 78 THR cc_start: 0.8177 (p) cc_final: 0.7870 (p) outliers start: 17 outliers final: 11 residues processed: 104 average time/residue: 0.2134 time to fit residues: 26.8168 Evaluate side-chains 89 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 107 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 46 optimal weight: 0.0170 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS A 518 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.066982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.060459 restraints weight = 16827.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.062040 restraints weight = 7935.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.063020 restraints weight = 4510.203| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4697 Z= 0.171 Angle : 0.870 8.123 6427 Z= 0.391 Chirality : 0.054 0.284 776 Planarity : 0.005 0.044 775 Dihedral : 25.259 122.875 1103 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 4.39 % Allowed : 14.02 % Favored : 81.59 % 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: -3.04 (0.33), residues: 542 helix: -3.46 (0.90), residues: 12 sheet: -1.13 (0.36), residues: 186 loop : -2.63 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 573 HIS 0.002 0.001 HIS A 406 PHE 0.015 0.002 PHE A 290 TYR 0.014 0.001 TYR B 80 ARG 0.011 0.001 ARG B 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00019 ( 1) link_NAG-ASN : angle 1.92979 ( 3) link_ALPHA1-6 : bond 0.01000 ( 7) link_ALPHA1-6 : angle 2.40685 ( 21) link_BETA1-4 : bond 0.00691 ( 10) link_BETA1-4 : angle 2.65320 ( 30) link_ALPHA1-3 : bond 0.01231 ( 3) link_ALPHA1-3 : angle 3.01405 ( 9) hydrogen bonds : bond 0.03294 ( 103) hydrogen bonds : angle 5.35196 ( 324) SS BOND : bond 0.00646 ( 8) SS BOND : angle 1.48920 ( 16) covalent geometry : bond 0.00384 ( 4668) covalent geometry : angle 0.83277 ( 6348) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7649 (tpp) cc_final: 0.7195 (tpp) REVERT: A 394 ASN cc_start: 0.8004 (m-40) cc_final: 0.7630 (m110) REVERT: A 463 MET cc_start: 0.8710 (mmt) cc_final: 0.8299 (mmt) REVERT: A 527 ASP cc_start: 0.7574 (p0) cc_final: 0.7343 (p0) REVERT: B 32 TYR cc_start: 0.7532 (m-10) cc_final: 0.7274 (m-10) outliers start: 21 outliers final: 10 residues processed: 98 average time/residue: 0.2012 time to fit residues: 24.1168 Evaluate side-chains 86 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 107 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 8 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.063585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.057293 restraints weight = 16856.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.058774 restraints weight = 7748.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.059764 restraints weight = 4376.403| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4697 Z= 0.190 Angle : 0.896 9.392 6427 Z= 0.396 Chirality : 0.055 0.316 776 Planarity : 0.005 0.044 775 Dihedral : 21.689 124.155 1103 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 3.97 % Allowed : 17.15 % Favored : 78.87 % 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: -2.77 (0.33), residues: 542 helix: -3.26 (0.85), residues: 12 sheet: -0.90 (0.37), residues: 185 loop : -2.47 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 573 HIS 0.002 0.001 HIS A 406 PHE 0.010 0.002 PHE A 290 TYR 0.015 0.002 TYR B 80 ARG 0.005 0.001 ARG A 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 1) link_NAG-ASN : angle 1.81176 ( 3) link_ALPHA1-6 : bond 0.01428 ( 7) link_ALPHA1-6 : angle 2.59416 ( 21) link_BETA1-4 : bond 0.00672 ( 10) link_BETA1-4 : angle 2.94950 ( 30) link_ALPHA1-3 : bond 0.01215 ( 3) link_ALPHA1-3 : angle 3.06055 ( 9) hydrogen bonds : bond 0.03066 ( 103) hydrogen bonds : angle 5.14885 ( 324) SS BOND : bond 0.00292 ( 8) SS BOND : angle 1.60791 ( 16) covalent geometry : bond 0.00420 ( 4668) covalent geometry : angle 0.85370 ( 6348) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.5898 (mtt) cc_final: 0.5589 (mtt) REVERT: A 463 MET cc_start: 0.8707 (mmt) cc_final: 0.8305 (mmt) outliers start: 19 outliers final: 15 residues processed: 92 average time/residue: 0.1939 time to fit residues: 21.9950 Evaluate side-chains 92 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 57 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 107 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 0.0470 chunk 22 optimal weight: 0.0470 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 3 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 = 0.3257 r_free = 0.3257 target = 0.061807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.055582 restraints weight = 17219.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.057094 restraints weight = 7777.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.058060 restraints weight = 4311.739| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4697 Z= 0.189 Angle : 0.896 8.900 6427 Z= 0.396 Chirality : 0.053 0.285 776 Planarity : 0.005 0.043 775 Dihedral : 19.564 125.486 1103 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 3.97 % Allowed : 17.36 % Favored : 78.66 % 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: -2.48 (0.34), residues: 542 helix: -2.76 (1.19), residues: 12 sheet: -0.67 (0.38), residues: 183 loop : -2.29 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 573 HIS 0.003 0.001 HIS A 406 PHE 0.013 0.002 PHE A 369 TYR 0.015 0.002 TYR B 80 ARG 0.005 0.001 ARG B 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 1) link_NAG-ASN : angle 1.90768 ( 3) link_ALPHA1-6 : bond 0.01400 ( 7) link_ALPHA1-6 : angle 2.28533 ( 21) link_BETA1-4 : bond 0.00693 ( 10) link_BETA1-4 : angle 3.14057 ( 30) link_ALPHA1-3 : bond 0.01328 ( 3) link_ALPHA1-3 : angle 2.88759 ( 9) hydrogen bonds : bond 0.03137 ( 103) hydrogen bonds : angle 5.10964 ( 324) SS BOND : bond 0.00177 ( 8) SS BOND : angle 1.48551 ( 16) covalent geometry : bond 0.00422 ( 4668) covalent geometry : angle 0.85425 ( 6348) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.6022 (mtt) cc_final: 0.5798 (mtt) REVERT: A 463 MET cc_start: 0.8730 (mmt) cc_final: 0.8345 (mmt) outliers start: 19 outliers final: 16 residues processed: 90 average time/residue: 0.2069 time to fit residues: 22.8770 Evaluate side-chains 90 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 107 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.061302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.055040 restraints weight = 16976.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.056554 restraints weight = 7646.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.057535 restraints weight = 4278.732| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4697 Z= 0.176 Angle : 0.883 9.389 6427 Z= 0.390 Chirality : 0.052 0.294 776 Planarity : 0.005 0.043 775 Dihedral : 17.935 126.023 1103 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 3.77 % Allowed : 17.99 % Favored : 78.24 % 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: -2.38 (0.34), residues: 542 helix: -2.76 (1.19), residues: 12 sheet: -0.60 (0.40), residues: 174 loop : -2.18 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 573 HIS 0.003 0.001 HIS A 333 PHE 0.011 0.002 PHE B 27 TYR 0.012 0.001 TYR B 80 ARG 0.008 0.001 ARG A 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00145 ( 1) link_NAG-ASN : angle 1.98332 ( 3) link_ALPHA1-6 : bond 0.01553 ( 7) link_ALPHA1-6 : angle 2.21128 ( 21) link_BETA1-4 : bond 0.00719 ( 10) link_BETA1-4 : angle 3.30591 ( 30) link_ALPHA1-3 : bond 0.01374 ( 3) link_ALPHA1-3 : angle 2.68752 ( 9) hydrogen bonds : bond 0.02949 ( 103) hydrogen bonds : angle 5.03431 ( 324) SS BOND : bond 0.00195 ( 8) SS BOND : angle 0.72698 ( 16) covalent geometry : bond 0.00389 ( 4668) covalent geometry : angle 0.84148 ( 6348) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.8790 (mmt) cc_final: 0.8385 (mmt) REVERT: B 32 TYR cc_start: 0.7353 (m-10) cc_final: 0.6859 (m-80) outliers start: 18 outliers final: 14 residues processed: 89 average time/residue: 0.2015 time to fit residues: 21.8987 Evaluate side-chains 85 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 107 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 3 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 = 0.3156 r_free = 0.3156 target = 0.057618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.051490 restraints weight = 17257.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.052962 restraints weight = 7782.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.053906 restraints weight = 4325.281| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 4697 Z= 0.233 Angle : 0.922 9.648 6427 Z= 0.418 Chirality : 0.052 0.315 776 Planarity : 0.005 0.042 775 Dihedral : 16.352 125.864 1103 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Rotamer: Outliers : 3.97 % Allowed : 18.62 % Favored : 77.41 % 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: -2.42 (0.34), residues: 542 helix: -3.19 (0.78), residues: 12 sheet: -0.59 (0.38), residues: 181 loop : -2.24 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 573 HIS 0.003 0.001 HIS A 233 PHE 0.018 0.003 PHE B 27 TYR 0.013 0.002 TYR A 547 ARG 0.009 0.001 ARG A 372 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 1) link_NAG-ASN : angle 1.88422 ( 3) link_ALPHA1-6 : bond 0.01430 ( 7) link_ALPHA1-6 : angle 2.21048 ( 21) link_BETA1-4 : bond 0.00776 ( 10) link_BETA1-4 : angle 3.55117 ( 30) link_ALPHA1-3 : bond 0.01345 ( 3) link_ALPHA1-3 : angle 2.54579 ( 9) hydrogen bonds : bond 0.03378 ( 103) hydrogen bonds : angle 5.19208 ( 324) SS BOND : bond 0.00493 ( 8) SS BOND : angle 1.04489 ( 16) covalent geometry : bond 0.00521 ( 4668) covalent geometry : angle 0.87831 ( 6348) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.8787 (mmt) cc_final: 0.8430 (mmt) REVERT: A 495 ARG cc_start: 0.7276 (mtm180) cc_final: 0.6629 (mtp85) REVERT: B 32 TYR cc_start: 0.7456 (m-10) cc_final: 0.6889 (m-80) REVERT: B 77 ASN cc_start: 0.8406 (m-40) cc_final: 0.8169 (t0) REVERT: B 83 MET cc_start: 0.8807 (mmm) cc_final: 0.8574 (mmm) outliers start: 19 outliers final: 14 residues processed: 86 average time/residue: 0.2473 time to fit residues: 25.5715 Evaluate side-chains 81 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 107 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3147 r_free = 0.3147 target = 0.057100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.050921 restraints weight = 17405.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.052378 restraints weight = 7884.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.053304 restraints weight = 4401.988| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4697 Z= 0.223 Angle : 0.931 12.624 6427 Z= 0.425 Chirality : 0.052 0.347 776 Planarity : 0.005 0.040 775 Dihedral : 15.698 124.207 1103 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.92 % Favored : 87.08 % Rotamer: Outliers : 3.14 % Allowed : 20.50 % Favored : 76.36 % 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: -2.49 (0.34), residues: 542 helix: -2.97 (0.87), residues: 12 sheet: -0.67 (0.38), residues: 177 loop : -2.26 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 573 HIS 0.004 0.001 HIS A 406 PHE 0.018 0.002 PHE B 27 TYR 0.013 0.002 TYR A 547 ARG 0.010 0.001 ARG A 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 1) link_NAG-ASN : angle 1.97435 ( 3) link_ALPHA1-6 : bond 0.01492 ( 7) link_ALPHA1-6 : angle 2.22072 ( 21) link_BETA1-4 : bond 0.00706 ( 10) link_BETA1-4 : angle 3.60873 ( 30) link_ALPHA1-3 : bond 0.01482 ( 3) link_ALPHA1-3 : angle 2.33998 ( 9) hydrogen bonds : bond 0.03299 ( 103) hydrogen bonds : angle 5.22242 ( 324) SS BOND : bond 0.00290 ( 8) SS BOND : angle 0.93828 ( 16) covalent geometry : bond 0.00496 ( 4668) covalent geometry : angle 0.88813 ( 6348) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.8766 (mmt) cc_final: 0.8380 (mmt) REVERT: B 32 TYR cc_start: 0.7410 (m-10) cc_final: 0.6905 (m-80) REVERT: B 77 ASN cc_start: 0.8414 (m-40) cc_final: 0.8057 (t0) REVERT: B 87 ARG cc_start: 0.8566 (mtm180) cc_final: 0.8020 (mtm-85) outliers start: 15 outliers final: 13 residues processed: 81 average time/residue: 0.2469 time to fit residues: 24.2669 Evaluate side-chains 82 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 107 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 50 optimal weight: 0.0870 chunk 34 optimal weight: 0.5980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.059190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.053072 restraints weight = 17189.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.054536 restraints weight = 7796.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.055501 restraints weight = 4328.826| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4697 Z= 0.162 Angle : 0.895 13.544 6427 Z= 0.408 Chirality : 0.052 0.367 776 Planarity : 0.005 0.042 775 Dihedral : 14.762 121.282 1103 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer: Outliers : 2.93 % Allowed : 20.50 % Favored : 76.57 % 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: -2.43 (0.34), residues: 542 helix: -2.70 (0.98), residues: 12 sheet: -0.69 (0.38), residues: 176 loop : -2.19 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 573 HIS 0.002 0.001 HIS A 333 PHE 0.009 0.001 PHE B 68 TYR 0.009 0.001 TYR A 547 ARG 0.010 0.001 ARG A 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00039 ( 1) link_NAG-ASN : angle 2.20777 ( 3) link_ALPHA1-6 : bond 0.01473 ( 7) link_ALPHA1-6 : angle 2.09458 ( 21) link_BETA1-4 : bond 0.00782 ( 10) link_BETA1-4 : angle 3.67115 ( 30) link_ALPHA1-3 : bond 0.01562 ( 3) link_ALPHA1-3 : angle 2.21757 ( 9) hydrogen bonds : bond 0.03042 ( 103) hydrogen bonds : angle 5.14463 ( 324) SS BOND : bond 0.00161 ( 8) SS BOND : angle 0.68116 ( 16) covalent geometry : bond 0.00357 ( 4668) covalent geometry : angle 0.85005 ( 6348) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 315 MET cc_start: 0.7399 (ttm) cc_final: 0.7185 (ttm) REVERT: A 463 MET cc_start: 0.8762 (mmt) cc_final: 0.8372 (mmt) REVERT: B 32 TYR cc_start: 0.7114 (m-10) cc_final: 0.6542 (m-80) REVERT: B 77 ASN cc_start: 0.8282 (m-40) cc_final: 0.7960 (t0) REVERT: B 87 ARG cc_start: 0.8401 (mtm180) cc_final: 0.7975 (mtm-85) REVERT: B 89 GLU cc_start: 0.8493 (pm20) cc_final: 0.7728 (pm20) outliers start: 14 outliers final: 12 residues processed: 84 average time/residue: 0.2204 time to fit residues: 22.5049 Evaluate side-chains 81 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 107 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 30 optimal weight: 0.0970 chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- 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 = 0.3185 r_free = 0.3185 target = 0.058419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.052349 restraints weight = 17273.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.053778 restraints weight = 7931.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.054651 restraints weight = 4468.777| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4697 Z= 0.198 Angle : 0.924 10.371 6427 Z= 0.428 Chirality : 0.053 0.358 776 Planarity : 0.009 0.156 775 Dihedral : 14.465 121.940 1103 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.39 % Favored : 85.61 % Rotamer: Outliers : 2.72 % Allowed : 20.71 % Favored : 76.57 % 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: -2.40 (0.34), residues: 542 helix: -2.44 (1.11), residues: 12 sheet: -0.67 (0.38), residues: 179 loop : -2.19 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 573 HIS 0.002 0.001 HIS A 233 PHE 0.024 0.002 PHE A 290 TYR 0.021 0.002 TYR A 407 ARG 0.021 0.001 ARG A 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 1) link_NAG-ASN : angle 2.04068 ( 3) link_ALPHA1-6 : bond 0.01389 ( 7) link_ALPHA1-6 : angle 2.11693 ( 21) link_BETA1-4 : bond 0.00778 ( 10) link_BETA1-4 : angle 3.72102 ( 30) link_ALPHA1-3 : bond 0.01361 ( 3) link_ALPHA1-3 : angle 2.17562 ( 9) hydrogen bonds : bond 0.03290 ( 103) hydrogen bonds : angle 5.33677 ( 324) SS BOND : bond 0.00226 ( 8) SS BOND : angle 0.76142 ( 16) covalent geometry : bond 0.00442 ( 4668) covalent geometry : angle 0.88006 ( 6348) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 463 MET cc_start: 0.8772 (mmt) cc_final: 0.8405 (mmt) REVERT: B 77 ASN cc_start: 0.8317 (m-40) cc_final: 0.7997 (t0) REVERT: B 81 LEU cc_start: 0.8758 (tp) cc_final: 0.8544 (tt) outliers start: 13 outliers final: 12 residues processed: 79 average time/residue: 0.2002 time to fit residues: 19.6279 Evaluate side-chains 82 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 107 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3188 r_free = 0.3188 target = 0.058499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.052410 restraints weight = 17233.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.053825 restraints weight = 7968.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.054748 restraints weight = 4498.567| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.5928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4697 Z= 0.185 Angle : 0.927 14.423 6427 Z= 0.424 Chirality : 0.052 0.360 776 Planarity : 0.007 0.119 775 Dihedral : 14.081 118.268 1103 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.84 % Favored : 86.16 % Rotamer: Outliers : 2.72 % Allowed : 21.13 % Favored : 76.15 % 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: -2.44 (0.34), residues: 542 helix: -2.22 (1.19), residues: 12 sheet: -0.61 (0.39), residues: 175 loop : -2.27 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 573 HIS 0.003 0.001 HIS A 406 PHE 0.018 0.002 PHE A 290 TYR 0.010 0.001 TYR A 547 ARG 0.008 0.001 ARG B 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 1) link_NAG-ASN : angle 1.86505 ( 3) link_ALPHA1-6 : bond 0.01411 ( 7) link_ALPHA1-6 : angle 2.12580 ( 21) link_BETA1-4 : bond 0.00791 ( 10) link_BETA1-4 : angle 3.71407 ( 30) link_ALPHA1-3 : bond 0.01305 ( 3) link_ALPHA1-3 : angle 2.24268 ( 9) hydrogen bonds : bond 0.03119 ( 103) hydrogen bonds : angle 5.28097 ( 324) SS BOND : bond 0.00189 ( 8) SS BOND : angle 0.76343 ( 16) covalent geometry : bond 0.00412 ( 4668) covalent geometry : angle 0.88266 ( 6348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1805.38 seconds wall clock time: 32 minutes 3.48 seconds (1923.48 seconds total)