Starting phenix.real_space_refine on Tue Mar 3 15:52:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mgw_23830/03_2026/7mgw_23830.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mgw_23830/03_2026/7mgw_23830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mgw_23830/03_2026/7mgw_23830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mgw_23830/03_2026/7mgw_23830.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mgw_23830/03_2026/7mgw_23830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mgw_23830/03_2026/7mgw_23830.map" } resolution = 3.5 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= 0.001 sd= 0.041 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: 5 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 C 4140 2.51 5 N 964 2.21 5 O 1084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6223 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4292 Classifications: {'peptide': 537} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 514} Chain: "B" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 160 Unusual residues: {' CL': 1, 'CLR': 1, 'D10': 1, 'D12': 4, 'HP6': 6, 'LNK': 1, 'SRO': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Time building chain proxies: 1.43, per 1000 atoms: 0.23 Number of scatterers: 6223 At special positions: 0 Unit cell: (69.336, 73.224, 121.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 34 16.00 O 1084 8.00 N 964 7.00 C 4140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " 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=3, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 240.6 milliseconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 7 sheets defined 54.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.846A pdb=" N PHE A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 114 through 120 removed outlier: 3.809A pdb=" N LEU A 118 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU A 119 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Proline residue: A 120 - end of helix Processing helix chain 'A' and resid 121 through 144 Proline residue: A 131 - end of helix Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.524A pdb=" N TRP A 151 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.598A pdb=" N LYS A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 190 removed outlier: 4.145A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.668A pdb=" N HIS A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 252 through 272 removed outlier: 4.364A pdb=" N LYS A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.642A pdb=" N VAL A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TRP A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 300 removed outlier: 4.228A pdb=" N TYR A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 325 through 338 Processing helix chain 'A' and resid 342 through 349 Processing helix chain 'A' and resid 356 through 391 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.783A pdb=" N GLU A 396 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 397 " --> pdb=" O VAL A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 403 through 417 removed outlier: 4.749A pdb=" N PHE A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 454 removed outlier: 3.807A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 461 removed outlier: 4.511A pdb=" N LYS A 460 " --> pdb=" O HIS A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 482 removed outlier: 3.852A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 removed outlier: 4.318A pdb=" N VAL A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 Processing helix chain 'A' and resid 517 through 530 removed outlier: 4.432A pdb=" N ASP A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLU A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 543 through 559 Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 603 through 612 Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 25 removed outlier: 3.515A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 30 removed outlier: 5.352A pdb=" N GLU B 29 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 112 " --> pdb=" O GLN B 58 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 69 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 30 removed outlier: 5.352A pdb=" N GLU B 29 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 112 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.616A pdb=" N ALA C 39 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS C 43 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE C 95 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR C 94 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'C' and resid 50 through 51 removed outlier: 3.605A pdb=" N ASN C 51 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 removed outlier: 6.930A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C 121 " --> pdb=" O GLN C 114 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 912 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: 0.96 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1816 1.34 - 1.46: 1680 1.46 - 1.58: 2849 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6394 Sorted by residual: bond pdb=" CD1 SRO A 712 " pdb=" NE1 SRO A 712 " ideal model delta sigma weight residual 1.377 1.324 0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" CD1 SRO A 715 " pdb=" NE1 SRO A 715 " ideal model delta sigma weight residual 1.377 1.324 0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" CD2 SRO A 712 " pdb=" CE2 SRO A 712 " ideal model delta sigma weight residual 1.419 1.370 0.049 2.00e-02 2.50e+03 6.00e+00 bond pdb=" CD2 SRO A 715 " pdb=" CE2 SRO A 715 " ideal model delta sigma weight residual 1.419 1.370 0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" CB SRO A 715 " pdb=" CG SRO A 715 " ideal model delta sigma weight residual 1.498 1.527 -0.029 2.00e-02 2.50e+03 2.14e+00 ... (remaining 6389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 8486 2.07 - 4.13: 161 4.13 - 6.20: 16 6.20 - 8.27: 1 8.27 - 10.34: 1 Bond angle restraints: 8665 Sorted by residual: angle pdb=" C GLU C 47 " pdb=" N SER C 48 " pdb=" CA SER C 48 " ideal model delta sigma weight residual 121.70 132.04 -10.34 1.80e+00 3.09e-01 3.30e+01 angle pdb=" C LEU A 119 " pdb=" N PRO A 120 " pdb=" CA PRO A 120 " ideal model delta sigma weight residual 121.65 119.11 2.54 1.01e+00 9.80e-01 6.34e+00 angle pdb=" CA GLU C 47 " pdb=" C GLU C 47 " pdb=" N SER C 48 " ideal model delta sigma weight residual 115.60 118.96 -3.36 1.48e+00 4.57e-01 5.16e+00 angle pdb=" C20 CLR A 716 " pdb=" C22 CLR A 716 " pdb=" C23 CLR A 716 " ideal model delta sigma weight residual 115.57 109.14 6.43 3.00e+00 1.11e-01 4.59e+00 angle pdb=" N VAL A 236 " pdb=" CA VAL A 236 " pdb=" C VAL A 236 " ideal model delta sigma weight residual 113.39 110.26 3.13 1.47e+00 4.63e-01 4.53e+00 ... (remaining 8660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.03: 3447 19.03 - 38.06: 230 38.06 - 57.09: 37 57.09 - 76.11: 5 76.11 - 95.14: 10 Dihedral angle restraints: 3729 sinusoidal: 1529 harmonic: 2200 Sorted by residual: dihedral pdb=" C2 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" C5 NAG D 1 " ideal model delta sinusoidal sigma weight residual 53.78 -41.36 95.14 1 3.00e+01 1.11e-03 1.16e+01 dihedral pdb=" C2 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" O4 NAG D 1 " ideal model delta sinusoidal sigma weight residual 175.11 81.72 93.39 1 3.00e+01 1.11e-03 1.13e+01 dihedral pdb=" C5 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C4 NAG D 1 " pdb=" O3 NAG D 1 " ideal model delta sinusoidal sigma weight residual -174.13 -81.26 -92.87 1 3.00e+01 1.11e-03 1.12e+01 ... (remaining 3726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 869 0.068 - 0.137: 74 0.137 - 0.205: 2 0.205 - 0.273: 2 0.273 - 0.341: 1 Chirality restraints: 948 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.95e+01 chirality pdb=" C14 CLR A 716 " pdb=" C13 CLR A 716 " pdb=" C15 CLR A 716 " pdb=" C8 CLR A 716 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C9 CLR A 716 " pdb=" C10 CLR A 716 " pdb=" C11 CLR A 716 " pdb=" C8 CLR A 716 " both_signs ideal model delta sigma weight residual False -2.45 -2.68 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 945 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 570 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 571 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 571 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 571 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 100 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.48e+00 pdb=" N PRO C 101 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 101 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 101 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 589 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO A 590 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 590 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 590 " 0.015 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1875 2.81 - 3.34: 5836 3.34 - 3.86: 10538 3.86 - 4.38: 11412 4.38 - 4.90: 19850 Nonbonded interactions: 49511 Sorted by model distance: nonbonded pdb=" OG1 THR B 106 " pdb=" OD1 ASP B 109 " model vdw 2.292 3.040 nonbonded pdb=" O ILE A 108 " pdb=" ND2 ASN A 112 " model vdw 2.297 3.120 nonbonded pdb=" OG SER C 76 " pdb=" OD1 ASN C 77 " model vdw 2.310 3.040 nonbonded pdb=" OG SER C 55 " pdb=" O ALA C 74 " model vdw 2.313 3.040 nonbonded pdb=" O SER A 190 " pdb=" OG SER A 190 " model vdw 2.323 3.040 ... (remaining 49506 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.820 Find NCS groups from input model: 0.020 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6402 Z= 0.144 Angle : 0.646 10.607 8677 Z= 0.303 Chirality : 0.041 0.341 948 Planarity : 0.003 0.031 1049 Dihedral : 13.533 95.142 2324 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.40 % Allowed : 9.66 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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 are not related in a simple way. whole: -2.49 (0.28), residues: 759 helix: -0.76 (0.23), residues: 354 sheet: -1.78 (0.51), residues: 93 loop : -2.62 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 564 TYR 0.009 0.000 TYR A 176 PHE 0.015 0.001 PHE A 474 TRP 0.006 0.000 TRP A 317 HIS 0.001 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6394) covalent geometry : angle 0.63619 ( 8665) SS BOND : bond 0.00154 ( 3) SS BOND : angle 0.24093 ( 6) hydrogen bonds : bond 0.11025 ( 318) hydrogen bonds : angle 5.13441 ( 912) Misc. bond : bond 0.00043 ( 3) link_BETA1-4 : bond 0.06372 ( 1) link_BETA1-4 : angle 6.18196 ( 3) link_NAG-ASN : bond 0.00526 ( 1) link_NAG-ASN : angle 1.21940 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.189 Fit side-chains REVERT: A 144 ARG cc_start: 0.6293 (mtm110) cc_final: 0.6074 (ttm110) REVERT: A 145 ASN cc_start: 0.6110 (t0) cc_final: 0.5464 (t0) REVERT: A 243 LYS cc_start: 0.7231 (mtmm) cc_final: 0.7008 (mmtm) REVERT: A 267 TYR cc_start: 0.5156 (t80) cc_final: 0.4873 (t80) REVERT: A 370 MET cc_start: 0.6126 (mmp) cc_final: 0.4205 (ttm) REVERT: A 391 ASN cc_start: 0.7447 (t0) cc_final: 0.7161 (t0) REVERT: A 430 MET cc_start: 0.6275 (ttm) cc_final: 0.6050 (tmm) REVERT: A 466 VAL cc_start: 0.3865 (p) cc_final: 0.3450 (t) REVERT: A 508 GLU cc_start: 0.6099 (tm-30) cc_final: 0.5663 (tm-30) REVERT: A 572 TYR cc_start: 0.6178 (t80) cc_final: 0.5765 (t80) REVERT: B 76 ASP cc_start: 0.7630 (t0) cc_final: 0.6898 (t0) REVERT: C 78 GLN cc_start: 0.7740 (mt0) cc_final: 0.7485 (mt0) outliers start: 9 outliers final: 4 residues processed: 151 average time/residue: 0.0819 time to fit residues: 15.7960 Evaluate side-chains 101 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN A 332 GLN A 355 ASN A 368 ASN B 25 GLN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN ** C 26 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 = 0.4293 r_free = 0.4293 target = 0.200157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.163855 restraints weight = 7698.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.169170 restraints weight = 4691.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.172236 restraints weight = 3420.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.174881 restraints weight = 2811.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.176212 restraints weight = 2437.610| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6402 Z= 0.165 Angle : 0.600 9.818 8677 Z= 0.305 Chirality : 0.042 0.194 948 Planarity : 0.004 0.031 1049 Dihedral : 9.141 76.120 1018 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.36 % Allowed : 17.45 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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 are not related in a simple way. whole: -1.64 (0.29), residues: 759 helix: 0.12 (0.25), residues: 354 sheet: -1.48 (0.50), residues: 96 loop : -2.39 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 564 TYR 0.015 0.001 TYR A 358 PHE 0.026 0.002 PHE A 428 TRP 0.023 0.002 TRP A 326 HIS 0.002 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6394) covalent geometry : angle 0.59348 ( 8665) SS BOND : bond 0.00038 ( 3) SS BOND : angle 0.33791 ( 6) hydrogen bonds : bond 0.03442 ( 318) hydrogen bonds : angle 4.45446 ( 912) Misc. bond : bond 0.00054 ( 3) link_BETA1-4 : bond 0.00457 ( 1) link_BETA1-4 : angle 4.52368 ( 3) link_NAG-ASN : bond 0.00007 ( 1) link_NAG-ASN : angle 1.72435 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.147 Fit side-chains REVERT: A 391 ASN cc_start: 0.6456 (t0) cc_final: 0.6164 (m-40) REVERT: A 478 LEU cc_start: 0.7525 (tt) cc_final: 0.7249 (tp) REVERT: A 508 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7358 (tm-30) outliers start: 28 outliers final: 15 residues processed: 121 average time/residue: 0.0697 time to fit residues: 11.3132 Evaluate side-chains 108 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 57 optimal weight: 0.0670 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN B 54 ASN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.188218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.149691 restraints weight = 7578.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.155036 restraints weight = 4656.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.158576 restraints weight = 3418.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.160556 restraints weight = 2800.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.162322 restraints weight = 2469.842| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6402 Z= 0.158 Angle : 0.579 9.945 8677 Z= 0.295 Chirality : 0.041 0.231 948 Planarity : 0.004 0.032 1049 Dihedral : 8.045 67.198 1016 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.52 % Allowed : 19.00 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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 are not related in a simple way. whole: -1.45 (0.29), residues: 759 helix: 0.14 (0.25), residues: 363 sheet: -1.20 (0.50), residues: 96 loop : -2.25 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 144 TYR 0.012 0.001 TYR C 73 PHE 0.018 0.002 PHE A 604 TRP 0.014 0.001 TRP A 271 HIS 0.005 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 6394) covalent geometry : angle 0.57224 ( 8665) SS BOND : bond 0.00060 ( 3) SS BOND : angle 0.32103 ( 6) hydrogen bonds : bond 0.03397 ( 318) hydrogen bonds : angle 4.39731 ( 912) Misc. bond : bond 0.00041 ( 3) link_BETA1-4 : bond 0.01129 ( 1) link_BETA1-4 : angle 4.55170 ( 3) link_NAG-ASN : bond 0.00518 ( 1) link_NAG-ASN : angle 1.89830 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.227 Fit side-chains REVERT: A 84 LYS cc_start: 0.7026 (pttm) cc_final: 0.6160 (ptpt) REVERT: A 279 LYS cc_start: 0.5305 (tptt) cc_final: 0.4694 (mtmm) REVERT: A 280 VAL cc_start: 0.4222 (OUTLIER) cc_final: 0.4009 (t) REVERT: A 391 ASN cc_start: 0.6609 (t0) cc_final: 0.6246 (m-40) REVERT: A 478 LEU cc_start: 0.7636 (tt) cc_final: 0.7411 (tp) REVERT: A 508 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7425 (tm-30) outliers start: 29 outliers final: 21 residues processed: 123 average time/residue: 0.0612 time to fit residues: 10.6825 Evaluate side-chains 121 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 22 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN A 177 ASN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.183335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.143306 restraints weight = 7591.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.148524 restraints weight = 4591.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.152090 restraints weight = 3385.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.154399 restraints weight = 2768.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155788 restraints weight = 2436.960| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6402 Z= 0.163 Angle : 0.588 9.974 8677 Z= 0.305 Chirality : 0.042 0.190 948 Planarity : 0.004 0.037 1049 Dihedral : 7.043 58.970 1016 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 6.39 % Allowed : 19.00 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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 are not related in a simple way. whole: -1.34 (0.30), residues: 759 helix: 0.24 (0.26), residues: 360 sheet: -1.14 (0.51), residues: 101 loop : -2.18 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 607 TYR 0.012 0.002 TYR C 73 PHE 0.025 0.002 PHE A 407 TRP 0.018 0.001 TRP A 271 HIS 0.007 0.001 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 6394) covalent geometry : angle 0.58138 ( 8665) SS BOND : bond 0.00969 ( 3) SS BOND : angle 0.24085 ( 6) hydrogen bonds : bond 0.03499 ( 318) hydrogen bonds : angle 4.53348 ( 912) Misc. bond : bond 0.00042 ( 3) link_BETA1-4 : bond 0.01407 ( 1) link_BETA1-4 : angle 4.53680 ( 3) link_NAG-ASN : bond 0.00453 ( 1) link_NAG-ASN : angle 2.11544 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.215 Fit side-chains REVERT: A 84 LYS cc_start: 0.7003 (pttm) cc_final: 0.6216 (ptpt) REVERT: A 259 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6632 (mm) REVERT: A 391 ASN cc_start: 0.6669 (t0) cc_final: 0.6242 (m-40) REVERT: A 454 PHE cc_start: 0.6480 (m-10) cc_final: 0.6273 (m-10) REVERT: A 508 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7494 (tm-30) outliers start: 41 outliers final: 27 residues processed: 133 average time/residue: 0.0619 time to fit residues: 11.5334 Evaluate side-chains 131 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 121 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN B 101 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.182616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142747 restraints weight = 7787.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147944 restraints weight = 4730.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151419 restraints weight = 3478.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.153718 restraints weight = 2855.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.154523 restraints weight = 2503.228| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6402 Z= 0.149 Angle : 0.590 9.951 8677 Z= 0.304 Chirality : 0.041 0.200 948 Planarity : 0.004 0.050 1049 Dihedral : 6.331 56.868 1016 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.92 % Allowed : 20.72 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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 are not related in a simple way. whole: -1.29 (0.30), residues: 759 helix: 0.23 (0.26), residues: 362 sheet: -1.01 (0.52), residues: 101 loop : -2.15 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.010 0.001 TYR C 73 PHE 0.025 0.002 PHE A 407 TRP 0.022 0.001 TRP A 220 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6394) covalent geometry : angle 0.58385 ( 8665) SS BOND : bond 0.00301 ( 3) SS BOND : angle 0.33992 ( 6) hydrogen bonds : bond 0.03412 ( 318) hydrogen bonds : angle 4.54756 ( 912) Misc. bond : bond 0.00041 ( 3) link_BETA1-4 : bond 0.01377 ( 1) link_BETA1-4 : angle 4.32661 ( 3) link_NAG-ASN : bond 0.00324 ( 1) link_NAG-ASN : angle 2.10471 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.7013 (pttm) cc_final: 0.6239 (ptpt) REVERT: A 220 TRP cc_start: 0.5760 (m-90) cc_final: 0.5410 (m-90) REVERT: A 259 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.6796 (mm) REVERT: A 391 ASN cc_start: 0.6683 (t0) cc_final: 0.6192 (m-40) REVERT: A 508 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7711 (tm-30) outliers start: 38 outliers final: 32 residues processed: 126 average time/residue: 0.0642 time to fit residues: 11.3521 Evaluate side-chains 135 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 42 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 0.0370 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 63 optimal weight: 0.2980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN A 567 GLN B 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.184166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.144920 restraints weight = 7642.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150245 restraints weight = 4562.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.153835 restraints weight = 3322.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.156131 restraints weight = 2707.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.157424 restraints weight = 2363.458| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6402 Z= 0.128 Angle : 0.571 9.884 8677 Z= 0.295 Chirality : 0.041 0.198 948 Planarity : 0.004 0.049 1049 Dihedral : 5.852 56.506 1016 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.92 % Allowed : 21.81 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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 are not related in a simple way. whole: -1.15 (0.30), residues: 759 helix: 0.30 (0.26), residues: 362 sheet: -0.92 (0.52), residues: 101 loop : -2.02 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.010 0.001 TYR A 110 PHE 0.019 0.001 PHE A 407 TRP 0.014 0.001 TRP A 220 HIS 0.002 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6394) covalent geometry : angle 0.56543 ( 8665) SS BOND : bond 0.00240 ( 3) SS BOND : angle 0.25980 ( 6) hydrogen bonds : bond 0.03196 ( 318) hydrogen bonds : angle 4.53992 ( 912) Misc. bond : bond 0.00044 ( 3) link_BETA1-4 : bond 0.01225 ( 1) link_BETA1-4 : angle 3.80987 ( 3) link_NAG-ASN : bond 0.00539 ( 1) link_NAG-ASN : angle 2.35476 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 84 LYS cc_start: 0.7021 (pttm) cc_final: 0.6310 (ptpt) REVERT: A 97 VAL cc_start: 0.7808 (p) cc_final: 0.7578 (m) REVERT: A 220 TRP cc_start: 0.5751 (m-90) cc_final: 0.5445 (m-90) REVERT: A 259 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6534 (mm) REVERT: A 282 TRP cc_start: 0.5554 (OUTLIER) cc_final: 0.4674 (m100) REVERT: A 391 ASN cc_start: 0.6671 (t0) cc_final: 0.6165 (m-40) REVERT: A 454 PHE cc_start: 0.6326 (m-10) cc_final: 0.6088 (m-10) REVERT: A 508 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7516 (tm-30) outliers start: 38 outliers final: 30 residues processed: 135 average time/residue: 0.0642 time to fit residues: 12.0961 Evaluate side-chains 133 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 282 TRP Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 66 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.0030 chunk 29 optimal weight: 0.5980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.184290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146091 restraints weight = 7591.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151086 restraints weight = 4660.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.154460 restraints weight = 3434.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156502 restraints weight = 2818.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.158099 restraints weight = 2485.453| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6402 Z= 0.126 Angle : 0.574 9.857 8677 Z= 0.297 Chirality : 0.040 0.205 948 Planarity : 0.004 0.049 1049 Dihedral : 5.653 54.420 1016 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.98 % Allowed : 22.12 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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 are not related in a simple way. whole: -1.07 (0.30), residues: 759 helix: 0.32 (0.26), residues: 362 sheet: -0.86 (0.52), residues: 101 loop : -1.92 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 144 TYR 0.010 0.001 TYR A 110 PHE 0.021 0.001 PHE A 422 TRP 0.014 0.001 TRP A 326 HIS 0.002 0.001 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6394) covalent geometry : angle 0.56932 ( 8665) SS BOND : bond 0.00146 ( 3) SS BOND : angle 0.26267 ( 6) hydrogen bonds : bond 0.03179 ( 318) hydrogen bonds : angle 4.55154 ( 912) Misc. bond : bond 0.00034 ( 3) link_BETA1-4 : bond 0.01057 ( 1) link_BETA1-4 : angle 3.22047 ( 3) link_NAG-ASN : bond 0.00477 ( 1) link_NAG-ASN : angle 2.51265 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 84 LYS cc_start: 0.6999 (pttm) cc_final: 0.6276 (ptpt) REVERT: A 97 VAL cc_start: 0.7807 (p) cc_final: 0.7557 (m) REVERT: A 200 CYS cc_start: 0.2170 (OUTLIER) cc_final: 0.0117 (t) REVERT: A 220 TRP cc_start: 0.5754 (m-90) cc_final: 0.5518 (m-90) REVERT: A 259 ILE cc_start: 0.7137 (OUTLIER) cc_final: 0.6500 (mm) REVERT: A 282 TRP cc_start: 0.5657 (OUTLIER) cc_final: 0.4813 (m100) REVERT: A 391 ASN cc_start: 0.6658 (t0) cc_final: 0.6159 (m-40) REVERT: A 454 PHE cc_start: 0.6466 (m-10) cc_final: 0.5996 (m-80) REVERT: A 508 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7692 (tm-30) outliers start: 32 outliers final: 24 residues processed: 126 average time/residue: 0.0685 time to fit residues: 12.2808 Evaluate side-chains 127 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 282 TRP Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 24 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN A 562 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.181921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143391 restraints weight = 7647.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.148439 restraints weight = 4628.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.151864 restraints weight = 3394.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.153859 restraints weight = 2789.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155557 restraints weight = 2462.573| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6402 Z= 0.137 Angle : 0.579 9.881 8677 Z= 0.302 Chirality : 0.040 0.219 948 Planarity : 0.004 0.049 1049 Dihedral : 5.609 53.180 1016 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.83 % Allowed : 21.96 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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 are not related in a simple way. whole: -0.98 (0.30), residues: 759 helix: 0.38 (0.26), residues: 361 sheet: -0.83 (0.53), residues: 101 loop : -1.84 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 523 TYR 0.012 0.001 TYR A 110 PHE 0.023 0.001 PHE A 407 TRP 0.012 0.001 TRP A 326 HIS 0.002 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6394) covalent geometry : angle 0.57453 ( 8665) SS BOND : bond 0.00269 ( 3) SS BOND : angle 0.29810 ( 6) hydrogen bonds : bond 0.03194 ( 318) hydrogen bonds : angle 4.54823 ( 912) Misc. bond : bond 0.00034 ( 3) link_BETA1-4 : bond 0.00960 ( 1) link_BETA1-4 : angle 2.83266 ( 3) link_NAG-ASN : bond 0.00426 ( 1) link_NAG-ASN : angle 2.78500 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 84 LYS cc_start: 0.7028 (pttm) cc_final: 0.6315 (ptpt) REVERT: A 220 TRP cc_start: 0.5758 (m-90) cc_final: 0.5517 (m-90) REVERT: A 259 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.6608 (mm) REVERT: A 282 TRP cc_start: 0.5744 (OUTLIER) cc_final: 0.4957 (m100) REVERT: A 289 TYR cc_start: 0.6711 (m-10) cc_final: 0.6413 (m-80) REVERT: A 391 ASN cc_start: 0.6678 (t0) cc_final: 0.6172 (m-40) REVERT: A 454 PHE cc_start: 0.6583 (m-10) cc_final: 0.6166 (m-80) outliers start: 31 outliers final: 29 residues processed: 121 average time/residue: 0.0693 time to fit residues: 11.7389 Evaluate side-chains 126 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 282 TRP Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 12 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN C 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.180717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142210 restraints weight = 7667.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.147291 restraints weight = 4616.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.150671 restraints weight = 3384.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.152608 restraints weight = 2769.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.154305 restraints weight = 2445.419| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6402 Z= 0.143 Angle : 0.586 9.937 8677 Z= 0.306 Chirality : 0.041 0.227 948 Planarity : 0.004 0.050 1049 Dihedral : 5.626 52.022 1016 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 5.14 % Allowed : 21.65 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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 are not related in a simple way. whole: -1.01 (0.30), residues: 759 helix: 0.30 (0.26), residues: 367 sheet: -0.82 (0.53), residues: 97 loop : -1.81 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 607 TYR 0.013 0.001 TYR A 110 PHE 0.030 0.001 PHE A 407 TRP 0.013 0.001 TRP A 151 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6394) covalent geometry : angle 0.58182 ( 8665) SS BOND : bond 0.00274 ( 3) SS BOND : angle 0.32838 ( 6) hydrogen bonds : bond 0.03281 ( 318) hydrogen bonds : angle 4.56161 ( 912) Misc. bond : bond 0.00034 ( 3) link_BETA1-4 : bond 0.00931 ( 1) link_BETA1-4 : angle 2.60941 ( 3) link_NAG-ASN : bond 0.00407 ( 1) link_NAG-ASN : angle 2.93681 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 84 LYS cc_start: 0.7002 (pttm) cc_final: 0.6290 (ptpt) REVERT: A 220 TRP cc_start: 0.5792 (m-90) cc_final: 0.5568 (m-90) REVERT: A 259 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.6789 (mm) REVERT: A 282 TRP cc_start: 0.5788 (OUTLIER) cc_final: 0.5019 (m100) REVERT: A 391 ASN cc_start: 0.6670 (t0) cc_final: 0.6166 (m-40) REVERT: A 508 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7717 (tm-30) outliers start: 33 outliers final: 30 residues processed: 123 average time/residue: 0.0636 time to fit residues: 11.1057 Evaluate side-chains 126 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 282 TRP Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 59 optimal weight: 0.0670 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN C 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.178918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139609 restraints weight = 7654.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.144866 restraints weight = 4589.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.148308 restraints weight = 3349.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150518 restraints weight = 2745.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151712 restraints weight = 2413.119| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6402 Z= 0.154 Angle : 0.602 10.056 8677 Z= 0.313 Chirality : 0.041 0.241 948 Planarity : 0.004 0.051 1049 Dihedral : 5.706 51.036 1016 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.83 % Allowed : 22.27 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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 are not related in a simple way. whole: -1.05 (0.30), residues: 759 helix: 0.25 (0.26), residues: 367 sheet: -0.76 (0.54), residues: 96 loop : -1.83 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 523 TYR 0.012 0.001 TYR A 110 PHE 0.030 0.001 PHE A 407 TRP 0.015 0.001 TRP A 151 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 6394) covalent geometry : angle 0.59781 ( 8665) SS BOND : bond 0.00287 ( 3) SS BOND : angle 0.29382 ( 6) hydrogen bonds : bond 0.03364 ( 318) hydrogen bonds : angle 4.62110 ( 912) Misc. bond : bond 0.00036 ( 3) link_BETA1-4 : bond 0.00890 ( 1) link_BETA1-4 : angle 2.38182 ( 3) link_NAG-ASN : bond 0.00398 ( 1) link_NAG-ASN : angle 3.19807 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.7019 (pttm) cc_final: 0.6311 (ptpt) REVERT: A 97 VAL cc_start: 0.7893 (p) cc_final: 0.7653 (m) REVERT: A 101 ASN cc_start: 0.4322 (OUTLIER) cc_final: 0.2521 (t0) REVERT: A 220 TRP cc_start: 0.5832 (m-90) cc_final: 0.5539 (m-90) REVERT: A 259 ILE cc_start: 0.7320 (OUTLIER) cc_final: 0.6980 (mm) REVERT: A 282 TRP cc_start: 0.5910 (OUTLIER) cc_final: 0.5108 (m100) REVERT: A 391 ASN cc_start: 0.6689 (t0) cc_final: 0.6142 (m-40) REVERT: A 508 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7742 (tm-30) REVERT: B 127 MET cc_start: 0.8308 (mtt) cc_final: 0.7973 (mtt) outliers start: 31 outliers final: 27 residues processed: 120 average time/residue: 0.0661 time to fit residues: 11.0774 Evaluate side-chains 124 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 282 TRP Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 CYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.178980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140349 restraints weight = 7652.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145297 restraints weight = 4743.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.148572 restraints weight = 3510.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.150742 restraints weight = 2887.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.151929 restraints weight = 2552.942| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6402 Z= 0.148 Angle : 0.594 10.035 8677 Z= 0.309 Chirality : 0.041 0.242 948 Planarity : 0.004 0.051 1049 Dihedral : 5.709 50.232 1016 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.83 % Allowed : 22.12 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.27 % 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 are not related in a simple way. whole: -1.07 (0.30), residues: 759 helix: 0.21 (0.26), residues: 368 sheet: -0.75 (0.54), residues: 96 loop : -1.83 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 523 TYR 0.013 0.001 TYR A 110 PHE 0.029 0.001 PHE A 407 TRP 0.015 0.001 TRP A 151 HIS 0.002 0.001 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6394) covalent geometry : angle 0.58976 ( 8665) SS BOND : bond 0.00287 ( 3) SS BOND : angle 0.32085 ( 6) hydrogen bonds : bond 0.03329 ( 318) hydrogen bonds : angle 4.62236 ( 912) Misc. bond : bond 0.00034 ( 3) link_BETA1-4 : bond 0.00909 ( 1) link_BETA1-4 : angle 2.31561 ( 3) link_NAG-ASN : bond 0.00418 ( 1) link_NAG-ASN : angle 3.26243 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1301.21 seconds wall clock time: 23 minutes 8.46 seconds (1388.46 seconds total)