Starting phenix.real_space_refine on Wed Sep 17 04:53:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xpy_38563/09_2025/8xpy_38563.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xpy_38563/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xpy_38563/09_2025/8xpy_38563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xpy_38563/09_2025/8xpy_38563.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xpy_38563/09_2025/8xpy_38563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xpy_38563/09_2025/8xpy_38563.map" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.024 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.33, per 1000 atoms: 0.29 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: 0.53 Conformation dependent library (CDL) restraints added in 183.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.14 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: 0.77 Time building geometry restraints manager: 0.67 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.210 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.050 ------------------------------------------------------------------------------- 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 : 10.22 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 258 TYR 0.004 0.001 TYR A 581 PHE 0.007 0.001 PHE A 466 TRP 0.006 0.001 TRP B 36 HIS 0.000 0.000 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 4668) covalent geometry : angle 0.78734 ( 6348) SS BOND : bond 0.00067 ( 8) SS BOND : angle 0.47994 ( 16) hydrogen bonds : bond 0.16409 ( 103) hydrogen bonds : angle 7.36745 ( 324) link_ALPHA1-3 : bond 0.00642 ( 3) link_ALPHA1-3 : angle 2.18136 ( 9) 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_NAG-ASN : bond 0.00535 ( 1) link_NAG-ASN : angle 2.56768 ( 3) *********************** 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 : 0.166 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: 0.1008 time to fit residues: 17.4029 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 : 0.155 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.067353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.060912 restraints weight = 16960.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.062478 restraints weight = 7888.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.063513 restraints weight = 4495.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.064179 restraints weight = 2939.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.064530 restraints weight = 2141.506| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4697 Z= 0.172 Angle : 0.910 8.957 6427 Z= 0.395 Chirality : 0.057 0.271 776 Planarity : 0.005 0.046 775 Dihedral : 29.683 115.280 1105 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 3.14 % Allowed : 14.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.40 (0.32), residues: 542 helix: -4.19 (0.34), residues: 12 sheet: -1.29 (0.36), residues: 188 loop : -2.92 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 402 TYR 0.015 0.002 TYR A 416 PHE 0.017 0.002 PHE B 27 TRP 0.016 0.002 TRP B 104 HIS 0.003 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 4668) covalent geometry : angle 0.87205 ( 6348) SS BOND : bond 0.00295 ( 8) SS BOND : angle 1.02870 ( 16) hydrogen bonds : bond 0.03595 ( 103) hydrogen bonds : angle 5.49770 ( 324) link_ALPHA1-3 : bond 0.01064 ( 3) link_ALPHA1-3 : angle 3.46536 ( 9) link_ALPHA1-6 : bond 0.00951 ( 7) link_ALPHA1-6 : angle 2.53264 ( 21) link_BETA1-4 : bond 0.00807 ( 10) link_BETA1-4 : angle 2.76067 ( 30) link_NAG-ASN : bond 0.00021 ( 1) link_NAG-ASN : angle 1.75717 ( 3) *********************** 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 110 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.7289 (ttm) cc_final: 0.6738 (ttm) REVERT: A 394 ASN cc_start: 0.7951 (m-40) cc_final: 0.7503 (m-40) REVERT: A 463 MET cc_start: 0.8634 (mmt) cc_final: 0.8173 (mmt) REVERT: B 32 TYR cc_start: 0.7447 (m-10) cc_final: 0.7051 (m-80) REVERT: B 78 THR cc_start: 0.8225 (p) cc_final: 0.7928 (p) outliers start: 15 outliers final: 8 residues processed: 104 average time/residue: 0.0901 time to fit residues: 11.3775 Evaluate side-chains 84 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 107 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.057855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.051549 restraints weight = 17011.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.052993 restraints weight = 7845.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.053936 restraints weight = 4457.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.054490 restraints weight = 2923.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.054918 restraints weight = 2184.845| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 4697 Z= 0.323 Angle : 1.017 7.913 6427 Z= 0.471 Chirality : 0.056 0.256 776 Planarity : 0.005 0.043 775 Dihedral : 25.624 126.973 1103 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 5.23 % Allowed : 15.48 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.17 (0.33), residues: 542 helix: -3.42 (0.78), residues: 12 sheet: -1.19 (0.38), residues: 182 loop : -2.73 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 396 TYR 0.020 0.003 TYR B 60 PHE 0.032 0.004 PHE B 27 TRP 0.033 0.003 TRP A 573 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00722 ( 4668) covalent geometry : angle 0.98447 ( 6348) SS BOND : bond 0.01668 ( 8) SS BOND : angle 1.01567 ( 16) hydrogen bonds : bond 0.03940 ( 103) hydrogen bonds : angle 6.00687 ( 324) link_ALPHA1-3 : bond 0.01015 ( 3) link_ALPHA1-3 : angle 3.28002 ( 9) link_ALPHA1-6 : bond 0.00805 ( 7) link_ALPHA1-6 : angle 2.51667 ( 21) link_BETA1-4 : bond 0.00623 ( 10) link_BETA1-4 : angle 2.81772 ( 30) link_NAG-ASN : bond 0.00681 ( 1) link_NAG-ASN : angle 1.46314 ( 3) *********************** 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 107 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7525 (tmm) REVERT: A 463 MET cc_start: 0.8662 (mmt) cc_final: 0.8303 (mmt) REVERT: B 81 LEU cc_start: 0.8900 (tp) cc_final: 0.8536 (tt) outliers start: 25 outliers final: 15 residues processed: 97 average time/residue: 0.0916 time to fit residues: 10.7107 Evaluate side-chains 88 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 386 LYS 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 B residue 11 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 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 2 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.059226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053031 restraints weight = 17016.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.054480 restraints weight = 7634.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.055426 restraints weight = 4271.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.056017 restraints weight = 2764.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.056458 restraints weight = 2039.476| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4697 Z= 0.182 Angle : 0.909 9.557 6427 Z= 0.402 Chirality : 0.054 0.300 776 Planarity : 0.005 0.044 775 Dihedral : 22.557 124.879 1103 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 3.77 % Allowed : 18.62 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (0.34), residues: 542 helix: -3.29 (0.66), residues: 12 sheet: -0.97 (0.39), residues: 180 loop : -2.39 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 242 TYR 0.021 0.002 TYR B 80 PHE 0.014 0.002 PHE A 290 TRP 0.016 0.002 TRP A 573 HIS 0.002 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 4668) covalent geometry : angle 0.86587 ( 6348) SS BOND : bond 0.00212 ( 8) SS BOND : angle 1.84711 ( 16) hydrogen bonds : bond 0.03238 ( 103) hydrogen bonds : angle 5.46144 ( 324) link_ALPHA1-3 : bond 0.01304 ( 3) link_ALPHA1-3 : angle 2.99310 ( 9) link_ALPHA1-6 : bond 0.01260 ( 7) link_ALPHA1-6 : angle 2.56415 ( 21) link_BETA1-4 : bond 0.00655 ( 10) link_BETA1-4 : angle 2.94171 ( 30) link_NAG-ASN : bond 0.00100 ( 1) link_NAG-ASN : angle 2.10246 ( 3) *********************** 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 95 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7376 (tmm) REVERT: A 318 ARG cc_start: 0.7337 (ttp-110) cc_final: 0.7021 (ttt-90) REVERT: A 463 MET cc_start: 0.8773 (mmt) cc_final: 0.8355 (mmt) REVERT: A 495 ARG cc_start: 0.7217 (mtm180) cc_final: 0.6626 (mtp85) REVERT: B 67 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7876 (mtp85) outliers start: 18 outliers final: 12 residues processed: 87 average time/residue: 0.0944 time to fit residues: 9.8397 Evaluate side-chains 87 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 351 TYR 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 B residue 11 LEU Chi-restraints excluded: chain B residue 67 ARG 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 40 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 0.0670 chunk 33 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 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 = 0.3156 r_free = 0.3156 target = 0.057738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.051724 restraints weight = 17119.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.053149 restraints weight = 7686.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.054011 restraints weight = 4284.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.054636 restraints weight = 2797.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.054909 restraints weight = 2030.758| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 4697 Z= 0.205 Angle : 0.925 9.228 6427 Z= 0.410 Chirality : 0.053 0.284 776 Planarity : 0.005 0.043 775 Dihedral : 20.599 126.556 1103 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 3.97 % Allowed : 19.04 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.34), residues: 542 helix: -3.06 (0.89), residues: 12 sheet: -0.84 (0.39), residues: 183 loop : -2.35 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 516 TYR 0.018 0.002 TYR A 407 PHE 0.011 0.002 PHE A 369 TRP 0.017 0.002 TRP A 573 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 4668) covalent geometry : angle 0.88224 ( 6348) SS BOND : bond 0.00267 ( 8) SS BOND : angle 1.56133 ( 16) hydrogen bonds : bond 0.03176 ( 103) hydrogen bonds : angle 5.36504 ( 324) link_ALPHA1-3 : bond 0.01176 ( 3) link_ALPHA1-3 : angle 2.88833 ( 9) link_ALPHA1-6 : bond 0.01421 ( 7) link_ALPHA1-6 : angle 2.49189 ( 21) link_BETA1-4 : bond 0.00667 ( 10) link_BETA1-4 : angle 3.12070 ( 30) link_NAG-ASN : bond 0.00143 ( 1) link_NAG-ASN : angle 2.29643 ( 3) *********************** 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 100 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7379 (tmm) REVERT: A 318 ARG cc_start: 0.7576 (ttp-110) cc_final: 0.7182 (ttt-90) REVERT: A 399 MET cc_start: 0.5908 (mtt) cc_final: 0.5704 (mtt) REVERT: A 463 MET cc_start: 0.8784 (mmt) cc_final: 0.8349 (mmt) REVERT: A 495 ARG cc_start: 0.7249 (mtm180) cc_final: 0.6614 (mtp85) REVERT: B 32 TYR cc_start: 0.7407 (m-80) cc_final: 0.6892 (m-80) REVERT: B 67 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7748 (mtp85) outliers start: 19 outliers final: 11 residues processed: 93 average time/residue: 0.0917 time to fit residues: 10.2696 Evaluate side-chains 91 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 351 TYR 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 67 ARG 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 32 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.0970 chunk 18 optimal weight: 0.6980 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 306 ASN A 406 HIS A 518 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.059154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.053030 restraints weight = 17432.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.054476 restraints weight = 7782.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.055374 restraints weight = 4336.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.055998 restraints weight = 2842.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.056412 restraints weight = 2071.931| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5181 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= 0.169 Angle : 0.925 10.298 6427 Z= 0.407 Chirality : 0.053 0.280 776 Planarity : 0.005 0.047 775 Dihedral : 18.717 125.620 1103 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 3.35 % Allowed : 21.34 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.34), residues: 542 helix: -3.13 (0.83), residues: 12 sheet: -0.82 (0.39), residues: 173 loop : -2.17 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 98 TYR 0.022 0.002 TYR A 407 PHE 0.012 0.002 PHE A 266 TRP 0.017 0.002 TRP A 573 HIS 0.002 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 4668) covalent geometry : angle 0.88191 ( 6348) SS BOND : bond 0.00146 ( 8) SS BOND : angle 1.48398 ( 16) hydrogen bonds : bond 0.03020 ( 103) hydrogen bonds : angle 5.26923 ( 324) link_ALPHA1-3 : bond 0.01386 ( 3) link_ALPHA1-3 : angle 2.71269 ( 9) link_ALPHA1-6 : bond 0.01604 ( 7) link_ALPHA1-6 : angle 2.42140 ( 21) link_BETA1-4 : bond 0.00747 ( 10) link_BETA1-4 : angle 3.24647 ( 30) link_NAG-ASN : bond 0.00084 ( 1) link_NAG-ASN : angle 2.42577 ( 3) *********************** 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 99 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7360 (tmm) REVERT: A 463 MET cc_start: 0.8815 (mmt) cc_final: 0.8417 (mmt) REVERT: B 29 PHE cc_start: 0.7230 (t80) cc_final: 0.6999 (t80) REVERT: B 57 TYR cc_start: 0.7387 (t80) cc_final: 0.7132 (t80) REVERT: B 67 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7577 (mtp85) outliers start: 16 outliers final: 13 residues processed: 91 average time/residue: 0.1051 time to fit residues: 11.5188 Evaluate side-chains 91 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 316 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 587 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 100 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 13 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 0.0040 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN A 518 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.058152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.052100 restraints weight = 17321.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.053549 restraints weight = 7760.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054480 restraints weight = 4317.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055078 restraints weight = 2790.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.055483 restraints weight = 2036.796| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4697 Z= 0.199 Angle : 0.929 10.053 6427 Z= 0.414 Chirality : 0.053 0.280 776 Planarity : 0.005 0.042 775 Dihedral : 17.536 125.619 1103 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 3.35 % Allowed : 22.38 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.34), residues: 542 helix: -3.01 (0.88), residues: 12 sheet: -0.76 (0.39), residues: 177 loop : -2.24 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 318 TYR 0.019 0.002 TYR B 32 PHE 0.013 0.002 PHE A 290 TRP 0.020 0.002 TRP A 573 HIS 0.002 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 4668) covalent geometry : angle 0.88607 ( 6348) SS BOND : bond 0.00225 ( 8) SS BOND : angle 1.02749 ( 16) hydrogen bonds : bond 0.03123 ( 103) hydrogen bonds : angle 5.23898 ( 324) link_ALPHA1-3 : bond 0.01359 ( 3) link_ALPHA1-3 : angle 2.69708 ( 9) link_ALPHA1-6 : bond 0.01640 ( 7) link_ALPHA1-6 : angle 2.36440 ( 21) link_BETA1-4 : bond 0.00745 ( 10) link_BETA1-4 : angle 3.39781 ( 30) link_NAG-ASN : bond 0.00081 ( 1) link_NAG-ASN : angle 2.28553 ( 3) *********************** 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 91 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7312 (tmm) REVERT: A 463 MET cc_start: 0.8831 (mmt) cc_final: 0.8438 (mmt) outliers start: 16 outliers final: 14 residues processed: 83 average time/residue: 0.1107 time to fit residues: 10.9821 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 : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 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 67 ARG Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 LEU 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 51 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.058057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.052001 restraints weight = 17637.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.053456 restraints weight = 7826.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.054382 restraints weight = 4332.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055003 restraints weight = 2800.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.055377 restraints weight = 2026.310| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4697 Z= 0.189 Angle : 0.920 9.610 6427 Z= 0.414 Chirality : 0.052 0.288 776 Planarity : 0.005 0.042 775 Dihedral : 16.383 123.604 1103 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer: Outliers : 4.60 % Allowed : 21.76 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.34), residues: 542 helix: -2.91 (0.90), residues: 12 sheet: -0.70 (0.39), residues: 177 loop : -2.17 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 318 TYR 0.012 0.001 TYR B 32 PHE 0.011 0.002 PHE A 369 TRP 0.021 0.002 TRP A 573 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 4668) covalent geometry : angle 0.87649 ( 6348) SS BOND : bond 0.00210 ( 8) SS BOND : angle 0.86724 ( 16) hydrogen bonds : bond 0.03143 ( 103) hydrogen bonds : angle 5.18977 ( 324) link_ALPHA1-3 : bond 0.01445 ( 3) link_ALPHA1-3 : angle 2.59091 ( 9) link_ALPHA1-6 : bond 0.01610 ( 7) link_ALPHA1-6 : angle 2.28343 ( 21) link_BETA1-4 : bond 0.00737 ( 10) link_BETA1-4 : angle 3.51943 ( 30) link_NAG-ASN : bond 0.00083 ( 1) link_NAG-ASN : angle 2.21619 ( 3) *********************** 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 96 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7260 (tmm) REVERT: A 389 TYR cc_start: 0.6669 (m-80) cc_final: 0.6369 (m-10) REVERT: A 463 MET cc_start: 0.8811 (mmt) cc_final: 0.8409 (mmt) outliers start: 22 outliers final: 16 residues processed: 86 average time/residue: 0.1036 time to fit residues: 10.7282 Evaluate side-chains 85 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET 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 547 TYR 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 54 SER Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 LEU 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 25 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3196 r_free = 0.3196 target = 0.058646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.052670 restraints weight = 17665.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.054075 restraints weight = 8054.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.054983 restraints weight = 4533.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.055521 restraints weight = 2961.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.055952 restraints weight = 2208.025| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4697 Z= 0.173 Angle : 0.901 9.876 6427 Z= 0.408 Chirality : 0.052 0.313 776 Planarity : 0.005 0.043 775 Dihedral : 15.394 122.403 1103 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 3.77 % Allowed : 22.80 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.34), residues: 542 helix: -2.66 (1.00), residues: 12 sheet: -0.79 (0.38), residues: 175 loop : -2.13 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 318 TYR 0.009 0.001 TYR A 547 PHE 0.007 0.001 PHE A 369 TRP 0.034 0.002 TRP A 573 HIS 0.001 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 4668) covalent geometry : angle 0.85571 ( 6348) SS BOND : bond 0.00185 ( 8) SS BOND : angle 0.76749 ( 16) hydrogen bonds : bond 0.03113 ( 103) hydrogen bonds : angle 5.21677 ( 324) link_ALPHA1-3 : bond 0.01610 ( 3) link_ALPHA1-3 : angle 2.37686 ( 9) link_ALPHA1-6 : bond 0.01575 ( 7) link_ALPHA1-6 : angle 2.19697 ( 21) link_BETA1-4 : bond 0.00755 ( 10) link_BETA1-4 : angle 3.61485 ( 30) link_NAG-ASN : bond 0.00037 ( 1) link_NAG-ASN : angle 2.33778 ( 3) *********************** 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: 18 poor density : 71 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7216 (tmm) REVERT: A 389 TYR cc_start: 0.6623 (m-80) cc_final: 0.6379 (m-10) REVERT: A 463 MET cc_start: 0.8798 (mmt) cc_final: 0.8416 (mmt) outliers start: 18 outliers final: 15 residues processed: 81 average time/residue: 0.0973 time to fit residues: 9.6115 Evaluate side-chains 83 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET 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 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 67 ARG Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 100 LEU 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 44 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3198 r_free = 0.3198 target = 0.058845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.052904 restraints weight = 17687.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.054307 restraints weight = 7970.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.055224 restraints weight = 4495.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.055791 restraints weight = 2918.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.056197 restraints weight = 2155.339| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4697 Z= 0.175 Angle : 0.897 10.074 6427 Z= 0.406 Chirality : 0.051 0.351 776 Planarity : 0.005 0.050 775 Dihedral : 14.656 122.477 1103 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.36 % Favored : 87.64 % Rotamer: Outliers : 3.56 % Allowed : 22.38 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.35), residues: 542 helix: -2.40 (1.05), residues: 12 sheet: -0.88 (0.38), residues: 173 loop : -2.08 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 318 TYR 0.013 0.002 TYR B 32 PHE 0.016 0.002 PHE A 290 TRP 0.031 0.002 TRP A 573 HIS 0.002 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 4668) covalent geometry : angle 0.85025 ( 6348) SS BOND : bond 0.00147 ( 8) SS BOND : angle 0.72773 ( 16) hydrogen bonds : bond 0.03074 ( 103) hydrogen bonds : angle 5.21517 ( 324) link_ALPHA1-3 : bond 0.01565 ( 3) link_ALPHA1-3 : angle 2.21849 ( 9) link_ALPHA1-6 : bond 0.01484 ( 7) link_ALPHA1-6 : angle 2.13307 ( 21) link_BETA1-4 : bond 0.00766 ( 10) link_BETA1-4 : angle 3.71694 ( 30) link_NAG-ASN : bond 0.00040 ( 1) link_NAG-ASN : angle 2.38682 ( 3) ********************** 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 87 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7229 (tmm) REVERT: A 463 MET cc_start: 0.8804 (mmt) cc_final: 0.8404 (mmt) REVERT: B 54 SER cc_start: 0.8800 (m) cc_final: 0.8598 (p) REVERT: B 77 ASN cc_start: 0.8227 (m-40) cc_final: 0.7960 (t0) outliers start: 17 outliers final: 13 residues processed: 79 average time/residue: 0.1006 time to fit residues: 9.6698 Evaluate side-chains 82 residues out of total 478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET 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 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 83 MET Chi-restraints excluded: chain B residue 100 LEU 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 4 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.058992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.052928 restraints weight = 17809.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054365 restraints weight = 8089.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.055261 restraints weight = 4543.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.055865 restraints weight = 2995.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.056255 restraints weight = 2198.988| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4697 Z= 0.181 Angle : 0.893 12.520 6427 Z= 0.406 Chirality : 0.051 0.363 776 Planarity : 0.005 0.041 775 Dihedral : 14.202 121.478 1103 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 3.14 % Allowed : 22.38 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.35), residues: 542 helix: -2.15 (1.14), residues: 12 sheet: -0.66 (0.38), residues: 180 loop : -2.05 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 67 TYR 0.011 0.001 TYR A 407 PHE 0.021 0.002 PHE A 290 TRP 0.033 0.002 TRP A 573 HIS 0.001 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 4668) covalent geometry : angle 0.84501 ( 6348) SS BOND : bond 0.00134 ( 8) SS BOND : angle 0.73508 ( 16) hydrogen bonds : bond 0.02996 ( 103) hydrogen bonds : angle 5.19988 ( 324) link_ALPHA1-3 : bond 0.01428 ( 3) link_ALPHA1-3 : angle 2.14021 ( 9) link_ALPHA1-6 : bond 0.01428 ( 7) link_ALPHA1-6 : angle 2.11288 ( 21) link_BETA1-4 : bond 0.00798 ( 10) link_BETA1-4 : angle 3.78207 ( 30) link_NAG-ASN : bond 0.00005 ( 1) link_NAG-ASN : angle 2.35809 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 957.14 seconds wall clock time: 17 minutes 16.02 seconds (1036.02 seconds total)