Starting phenix.real_space_refine on Mon Sep 23 18:45:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xpy_38563/09_2024/8xpy_38563.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xpy_38563/09_2024/8xpy_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xpy_38563/09_2024/8xpy_38563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xpy_38563/09_2024/8xpy_38563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xpy_38563/09_2024/8xpy_38563.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xpy_38563/09_2024/8xpy_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-5461/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: 3.56, per 1000 atoms: 0.78 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: 1.64 Conformation dependent library (CDL) restraints added in 557.9 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: 0.56 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: 1.26 Time building geometry restraints manager: 1.81 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: 1.150 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.400 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.740 ------------------------------------------------------------------------------- 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 4668 Z= 0.262 Angle : 0.787 8.461 6348 Z= 0.353 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 *********************** 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 fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 0.471 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: 0.2290 time to fit residues: 39.6061 Evaluate side-chains 91 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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: 0.5980 chunk 13 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4668 Z= 0.234 Angle : 0.872 8.742 6348 Z= 0.384 Chirality : 0.057 0.275 776 Planarity : 0.005 0.047 775 Dihedral : 29.227 115.394 1105 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 3.35 % Allowed : 14.02 % Favored : 82.64 % 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: -3.42 (0.32), residues: 542 helix: -4.26 (0.32), residues: 12 sheet: -1.35 (0.36), residues: 187 loop : -2.89 (0.29), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 104 HIS 0.003 0.001 HIS A 333 PHE 0.017 0.002 PHE B 27 TYR 0.015 0.002 TYR A 416 ARG 0.008 0.001 ARG A 402 *********************** 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 111 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.7361 (ttm) cc_final: 0.6789 (ttm) REVERT: A 394 ASN cc_start: 0.7971 (m-40) cc_final: 0.7500 (m-40) REVERT: A 463 MET cc_start: 0.8636 (mmt) cc_final: 0.8181 (mmt) REVERT: B 32 TYR cc_start: 0.7454 (m-10) cc_final: 0.7072 (m-80) REVERT: B 78 THR cc_start: 0.8209 (p) cc_final: 0.7896 (p) outliers start: 16 outliers final: 9 residues processed: 104 average time/residue: 0.2102 time to fit residues: 26.3555 Evaluate side-chains 84 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4668 Z= 0.271 Angle : 0.834 8.092 6348 Z= 0.385 Chirality : 0.054 0.294 776 Planarity : 0.005 0.045 775 Dihedral : 25.459 122.817 1103 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 4.39 % Allowed : 13.60 % Favored : 82.01 % 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: -3.06 (0.32), residues: 542 helix: -3.48 (0.87), residues: 12 sheet: -1.10 (0.37), residues: 184 loop : -2.66 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 573 HIS 0.002 0.001 HIS A 406 PHE 0.013 0.002 PHE B 27 TYR 0.013 0.001 TYR B 60 ARG 0.005 0.001 ARG B 67 *********************** 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 105 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7687 (tpp) cc_final: 0.7195 (tpp) REVERT: A 394 ASN cc_start: 0.8027 (m-40) cc_final: 0.7683 (m-40) REVERT: A 463 MET cc_start: 0.8718 (mmt) cc_final: 0.8283 (mmt) REVERT: A 527 ASP cc_start: 0.7651 (p0) cc_final: 0.7434 (p0) REVERT: B 32 TYR cc_start: 0.7697 (m-10) cc_final: 0.7328 (m-80) REVERT: B 57 TYR cc_start: 0.7045 (t80) cc_final: 0.6819 (t80) outliers start: 21 outliers final: 10 residues processed: 96 average time/residue: 0.2017 time to fit residues: 23.6778 Evaluate side-chains 84 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLN 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 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 47 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4668 Z= 0.273 Angle : 0.862 9.448 6348 Z= 0.389 Chirality : 0.054 0.315 776 Planarity : 0.005 0.047 775 Dihedral : 21.764 124.485 1103 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 4.18 % Allowed : 17.36 % Favored : 78.45 % 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: -2.65 (0.34), residues: 542 helix: -3.44 (0.74), residues: 12 sheet: -0.85 (0.37), residues: 191 loop : -2.36 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 573 HIS 0.002 0.001 HIS A 233 PHE 0.025 0.002 PHE B 27 TYR 0.008 0.002 TYR A 547 ARG 0.009 0.001 ARG B 67 *********************** 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 98 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.5952 (mtt) cc_final: 0.5673 (mtt) REVERT: A 463 MET cc_start: 0.8763 (mmt) cc_final: 0.8325 (mmt) REVERT: B 32 TYR cc_start: 0.7562 (m-10) cc_final: 0.7296 (m-80) REVERT: B 57 TYR cc_start: 0.7292 (t80) cc_final: 0.7018 (t80) outliers start: 20 outliers final: 15 residues processed: 88 average time/residue: 0.2070 time to fit residues: 22.2920 Evaluate side-chains 88 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 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 17 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 83 MET 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 29 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4668 Z= 0.285 Angle : 0.860 9.097 6348 Z= 0.389 Chirality : 0.053 0.278 776 Planarity : 0.005 0.043 775 Dihedral : 19.446 125.938 1103 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 5.02 % Allowed : 16.74 % 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: -2.51 (0.34), residues: 542 helix: -3.22 (0.94), residues: 12 sheet: -0.74 (0.39), residues: 175 loop : -2.23 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 104 HIS 0.003 0.001 HIS A 406 PHE 0.018 0.002 PHE B 27 TYR 0.010 0.001 TYR A 547 ARG 0.006 0.001 ARG B 67 *********************** 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 104 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 80 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ARG cc_start: 0.7484 (ttp-110) cc_final: 0.7064 (ttt-90) REVERT: A 463 MET cc_start: 0.8787 (mmt) cc_final: 0.8358 (mmt) REVERT: B 32 TYR cc_start: 0.7515 (m-10) cc_final: 0.7291 (m-10) REVERT: B 57 TYR cc_start: 0.7573 (t80) cc_final: 0.7301 (t80) outliers start: 24 outliers final: 17 residues processed: 95 average time/residue: 0.2134 time to fit residues: 25.2634 Evaluate side-chains 85 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 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 17 SER Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 54 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN A 406 HIS A 482 ASN ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 4668 Z= 0.428 Angle : 0.946 8.725 6348 Z= 0.439 Chirality : 0.054 0.284 776 Planarity : 0.005 0.042 775 Dihedral : 18.027 127.724 1103 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.65 % Favored : 86.35 % Rotamer: Outliers : 4.60 % Allowed : 18.41 % 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 (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: -2.47 (0.34), residues: 542 helix: -3.45 (0.72), residues: 12 sheet: -0.59 (0.39), residues: 179 loop : -2.29 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 573 HIS 0.004 0.002 HIS A 233 PHE 0.014 0.003 PHE B 68 TYR 0.019 0.002 TYR B 32 ARG 0.007 0.001 ARG B 38 *********************** 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 fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.8812 (mmt) cc_final: 0.8414 (mmt) outliers start: 22 outliers final: 17 residues processed: 91 average time/residue: 0.2195 time to fit residues: 24.1484 Evaluate side-chains 84 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 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 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 47 TRP Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 69 THR 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 29 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.0770 chunk 10 optimal weight: 0.5980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4668 Z= 0.244 Angle : 0.852 11.631 6348 Z= 0.391 Chirality : 0.051 0.303 776 Planarity : 0.004 0.044 775 Dihedral : 16.290 123.176 1103 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 3.14 % Allowed : 19.67 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.30 (0.69), residues: 12 sheet: -0.72 (0.39), residues: 175 loop : -2.14 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 573 HIS 0.001 0.001 HIS A 233 PHE 0.014 0.002 PHE B 27 TYR 0.011 0.001 TYR B 57 ARG 0.005 0.000 ARG B 67 *********************** 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 92 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.8814 (mmt) cc_final: 0.8380 (mmt) REVERT: B 34 MET cc_start: 0.7702 (tpp) cc_final: 0.7250 (tpp) REVERT: B 47 TRP cc_start: 0.7594 (OUTLIER) cc_final: 0.7314 (p-90) REVERT: B 83 MET cc_start: 0.8679 (mmm) cc_final: 0.8406 (mmm) outliers start: 15 outliers final: 13 residues processed: 85 average time/residue: 0.2324 time to fit residues: 23.9857 Evaluate side-chains 83 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 587 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 47 TRP 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 9 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 0.0030 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4668 Z= 0.275 Angle : 0.851 10.329 6348 Z= 0.397 Chirality : 0.052 0.329 776 Planarity : 0.005 0.043 775 Dihedral : 15.363 124.367 1103 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.65 % Favored : 86.35 % Rotamer: Outliers : 3.56 % Allowed : 21.13 % 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 (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: -2.37 (0.34), residues: 542 helix: -3.04 (0.84), residues: 12 sheet: -0.72 (0.39), residues: 177 loop : -2.09 (0.31), residues: 353 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 0.010 0.002 PHE A 369 TYR 0.011 0.001 TYR B 60 ARG 0.006 0.001 ARG B 87 *********************** 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 86 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 69 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.8817 (mmt) cc_final: 0.8421 (mmt) REVERT: B 47 TRP cc_start: 0.7605 (OUTLIER) cc_final: 0.7357 (p-90) REVERT: B 77 ASN cc_start: 0.8403 (m-40) cc_final: 0.8025 (t0) outliers start: 17 outliers final: 14 residues processed: 79 average time/residue: 0.2115 time to fit residues: 20.1925 Evaluate side-chains 80 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 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 47 TRP 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 20 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4668 Z= 0.249 Angle : 0.836 11.464 6348 Z= 0.390 Chirality : 0.051 0.367 776 Planarity : 0.006 0.095 775 Dihedral : 14.554 122.566 1103 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 3.14 % Allowed : 21.34 % Favored : 75.52 % 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: -2.32 (0.34), residues: 542 helix: -2.82 (0.95), residues: 12 sheet: -0.78 (0.39), residues: 174 loop : -2.00 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 573 HIS 0.002 0.001 HIS A 406 PHE 0.009 0.001 PHE B 27 TYR 0.010 0.001 TYR A 547 ARG 0.003 0.000 ARG A 516 *********************** 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 86 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.8819 (mmt) cc_final: 0.8390 (mmt) REVERT: B 47 TRP cc_start: 0.7606 (OUTLIER) cc_final: 0.7355 (p-90) REVERT: B 77 ASN cc_start: 0.8329 (m-40) cc_final: 0.8025 (t0) outliers start: 15 outliers final: 14 residues processed: 80 average time/residue: 0.2139 time to fit residues: 20.9110 Evaluate side-chains 84 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 47 TRP 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 52 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4668 Z= 0.250 Angle : 0.854 13.132 6348 Z= 0.398 Chirality : 0.051 0.357 776 Planarity : 0.005 0.063 775 Dihedral : 14.203 121.158 1103 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % Rotamer: Outliers : 2.93 % Allowed : 22.18 % Favored : 74.90 % 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: -2.23 (0.35), residues: 542 helix: -2.64 (1.02), residues: 12 sheet: -0.57 (0.39), residues: 180 loop : -2.05 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 573 HIS 0.001 0.001 HIS A 233 PHE 0.009 0.001 PHE A 369 TYR 0.014 0.001 TYR B 60 ARG 0.012 0.001 ARG B 98 ********************** 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 84 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7799 (mm-40) REVERT: A 463 MET cc_start: 0.8819 (mmt) cc_final: 0.8405 (mmt) REVERT: B 47 TRP cc_start: 0.7578 (OUTLIER) cc_final: 0.7323 (p-90) REVERT: B 77 ASN cc_start: 0.8305 (m-40) cc_final: 0.8037 (t0) REVERT: B 87 ARG cc_start: 0.8232 (mtm180) cc_final: 0.7791 (mtm-85) outliers start: 14 outliers final: 12 residues processed: 79 average time/residue: 0.2083 time to fit residues: 20.1646 Evaluate side-chains 81 residues out of total 478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 547 TYR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 47 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 43 optimal weight: 0.0270 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.0370 chunk 48 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.3316 ------------------------------------------------------------------------------- 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 = 0.3240 r_free = 0.3240 target = 0.060658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054527 restraints weight = 17109.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.056026 restraints weight = 7725.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.056983 restraints weight = 4282.401| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4668 Z= 0.213 Angle : 0.832 12.525 6348 Z= 0.387 Chirality : 0.051 0.362 776 Planarity : 0.005 0.054 775 Dihedral : 13.514 116.102 1103 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.36 % Favored : 87.64 % Rotamer: Outliers : 2.72 % Allowed : 22.59 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.28 (0.34), residues: 542 helix: -2.19 (1.17), residues: 12 sheet: -0.70 (0.39), residues: 171 loop : -2.02 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 573 HIS 0.002 0.000 HIS A 406 PHE 0.010 0.001 PHE B 68 TYR 0.017 0.001 TYR B 32 ARG 0.007 0.000 ARG B 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1408.37 seconds wall clock time: 25 minutes 49.86 seconds (1549.86 seconds total)