Starting phenix.real_space_refine on Wed Jul 1 23:58:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vbd_64920/07_2026/9vbd_64920.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vbd_64920/07_2026/9vbd_64920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vbd_64920/07_2026/9vbd_64920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vbd_64920/07_2026/9vbd_64920.map" model { file = "/net/cci-nas-00/data/ceres_data/9vbd_64920/07_2026/9vbd_64920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vbd_64920/07_2026/9vbd_64920.cif" } resolution = 3.26 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= 0.000 sd= 0.036 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 Cu 1 5.60 5 S 15 5.16 5 C 2708 2.51 5 N 670 2.21 5 O 849 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4243 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4038 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 40, 'TRANS': 480} Chain: "B" 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 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: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.16, per 1000 atoms: 0.27 Number of scatterers: 4243 At special positions: 0 Unit cell: (55.61, 85.49, 97.11, 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) Cu 1 28.99 S 15 16.00 O 849 8.00 N 670 7.00 C 2708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 395 " - pdb=" SG CYS A 405 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 434 " distance=2.03 Simple disulfide: pdb=" SG CYS A 424 " - pdb=" SG CYS A 436 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " BETA1-6 " BMA E 3 " - " BMA E 4 " NAG-ASN " NAG A1001 " - " ASN A 182 " " NAG A1002 " - " ASN A 217 " " NAG A1003 " - " ASN A 456 " " NAG B 1 " - " ASN A 523 " " NAG C 1 " - " ASN A 284 " " NAG D 1 " - " ASN A 264 " " NAG E 1 " - " ASN A 298 " " NAG F 1 " - " ASN A 411 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 155.5 milliseconds 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 5 sheets defined 23.6% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 26 through 40 removed outlier: 3.514A pdb=" N TRP A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 131 through 137 removed outlier: 3.669A pdb=" N ILE A 134 " --> pdb=" O PRO A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.529A pdb=" N PHE A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 removed outlier: 3.505A pdb=" N VAL A 241 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 265 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 332 through 336 Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.818A pdb=" N SER A 406 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 474 Processing helix chain 'A' and resid 510 through 523 Processing helix chain 'A' and resid 529 through 533 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.423A pdb=" N THR A 61 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N ILE A 93 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 68 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASP A 95 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE A 70 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A 94 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 119 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A 343 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 367 " --> pdb=" O ILE A 388 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 176 removed outlier: 4.253A pdb=" N GLY A 176 " --> pdb=" O LYS A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 232 removed outlier: 5.484A pdb=" N GLY A 232 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ASP A 257 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU A 254 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR A 279 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLY A 256 " --> pdb=" O THR A 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.790A pdb=" N GLY A 328 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 350 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR A 375 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLU A 352 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR A 377 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 354 " --> pdb=" O TYR A 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 478 through 488 removed outlier: 6.286A pdb=" N VAL A 481 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE A 502 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL A 483 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU A 500 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ASN A 485 " --> pdb=" O ASP A 498 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP A 498 " --> pdb=" O ASN A 485 " (cutoff:3.500A) 101 hydrogen bonds defined for protein. 195 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: 0.68 Time building geometry restraints manager: 0.58 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: 1324 1.34 - 1.46: 1010 1.46 - 1.58: 1986 1.58 - 1.70: 1 1.70 - 1.82: 21 Bond restraints: 4342 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" CA ASP A 359 " pdb=" CB ASP A 359 " ideal model delta sigma weight residual 1.539 1.640 -0.100 4.88e-02 4.20e+02 4.22e+00 bond pdb=" C1 BMA E 4 " pdb=" C2 BMA E 4 " ideal model delta sigma weight residual 1.519 1.552 -0.033 2.00e-02 2.50e+03 2.79e+00 ... (remaining 4337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 5722 1.74 - 3.47: 166 3.47 - 5.21: 20 5.21 - 6.95: 8 6.95 - 8.68: 2 Bond angle restraints: 5918 Sorted by residual: angle pdb=" C ASN A 411 " pdb=" CA ASN A 411 " pdb=" CB ASN A 411 " ideal model delta sigma weight residual 110.51 102.10 8.41 1.89e+00 2.80e-01 1.98e+01 angle pdb=" N ASN A 411 " pdb=" CA ASN A 411 " pdb=" CB ASN A 411 " ideal model delta sigma weight residual 110.42 116.81 -6.39 1.52e+00 4.33e-01 1.77e+01 angle pdb=" CA ASN A 411 " pdb=" CB ASN A 411 " pdb=" CG ASN A 411 " ideal model delta sigma weight residual 112.60 115.76 -3.16 1.00e+00 1.00e+00 9.98e+00 angle pdb=" C CYS A 421 " pdb=" N SER A 422 " pdb=" CA SER A 422 " ideal model delta sigma weight residual 120.68 125.45 -4.77 1.52e+00 4.33e-01 9.85e+00 angle pdb=" C3 NAG F 1 " pdb=" C4 NAG F 1 " pdb=" O4 NAG F 1 " ideal model delta sigma weight residual 107.29 115.97 -8.68 3.00e+00 1.11e-01 8.38e+00 ... (remaining 5913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 2611 23.42 - 46.85: 148 46.85 - 70.27: 25 70.27 - 93.69: 14 93.69 - 117.12: 11 Dihedral angle restraints: 2809 sinusoidal: 1306 harmonic: 1503 Sorted by residual: dihedral pdb=" CB CYS A 53 " pdb=" SG CYS A 53 " pdb=" SG CYS A 62 " pdb=" CB CYS A 62 " ideal model delta sinusoidal sigma weight residual 93.00 169.88 -76.88 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" CA ASN A 411 " pdb=" C ASN A 411 " pdb=" N THR A 412 " pdb=" CA THR A 412 " ideal model delta harmonic sigma weight residual 180.00 137.05 42.95 0 5.00e+00 4.00e-02 7.38e+01 dihedral pdb=" C1 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " pdb=" C4 NAG D 1 " ideal model delta sinusoidal sigma weight residual -64.11 53.01 -117.12 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 2806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 649 0.085 - 0.170: 62 0.170 - 0.254: 4 0.254 - 0.339: 3 0.339 - 0.424: 1 Chirality restraints: 719 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 523 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.82 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 298 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C5 BMA E 4 " pdb=" C4 BMA E 4 " pdb=" C6 BMA E 4 " pdb=" O5 BMA E 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 716 not shown) Planarity restraints: 755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 411 " 0.035 2.00e-02 2.50e+03 3.37e-02 1.42e+01 pdb=" CG ASN A 411 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN A 411 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 411 " -0.015 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 523 " -0.029 2.00e-02 2.50e+03 2.74e-02 9.36e+00 pdb=" CG ASN A 523 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 523 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 523 " 0.034 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 411 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.77e+00 pdb=" CG ASN A 411 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 411 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 411 " 0.017 2.00e-02 2.50e+03 ... (remaining 752 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 116 2.69 - 3.24: 4238 3.24 - 3.80: 6489 3.80 - 4.35: 9063 4.35 - 4.90: 14672 Nonbonded interactions: 34578 Sorted by model distance: nonbonded pdb=" O PRO A 108 " pdb=" OG SER A 133 " model vdw 2.139 3.040 nonbonded pdb=" ND1 HIS A 222 " pdb="CU CU A1004 " model vdw 2.164 3.060 nonbonded pdb=" NE2 HIS A 199 " pdb="CU CU A1004 " model vdw 2.170 3.060 nonbonded pdb=" OD2 ASP A 95 " pdb=" OG SER A 522 " model vdw 2.179 3.040 nonbonded pdb=" OE2 GLU A 429 " pdb=" NH1 ARG A 484 " model vdw 2.206 3.120 ... (remaining 34573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.250 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 4361 Z= 0.209 Angle : 0.819 16.316 5971 Z= 0.364 Chirality : 0.055 0.424 719 Planarity : 0.005 0.039 747 Dihedral : 17.289 117.117 1829 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.98 (0.38), residues: 519 helix: -1.43 (0.51), residues: 105 sheet: -2.93 (0.48), residues: 104 loop : -0.55 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 484 TYR 0.010 0.001 TYR A 261 PHE 0.010 0.001 PHE A 440 TRP 0.017 0.001 TRP A 166 HIS 0.008 0.002 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 ( 4342) covalent geometry : angle 0.70088 / 0.34 ( 5918) SS BOND : bond 0.00103 / 0.05 ( 4) SS BOND : angle 1.05665 / 0.53 ( 8) hydrogen bonds : bond 0.18683 / 13.04 ( 101) hydrogen bonds : angle 6.42960 / 4.82 ( 195) link_BETA1-4 : bond 0.01292 / 0.62 ( 6) link_BETA1-4 : angle 5.79018 / 4.53 ( 18) link_BETA1-6 : bond 0.00455 / 0.24 ( 1) link_BETA1-6 : angle 1.53836 / 0.91 ( 3) link_NAG-ASN : bond 0.00703 / 0.43 ( 8) link_NAG-ASN : angle 4.44503 / 2.75 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.159 Fit side-chains REVERT: A 194 GLN cc_start: 0.7562 (mm110) cc_final: 0.7202 (mm-40) REVERT: A 234 ILE cc_start: 0.6904 (mt) cc_final: 0.6688 (mt) REVERT: A 349 SER cc_start: 0.7398 (m) cc_final: 0.6979 (t) REVERT: A 438 TYR cc_start: 0.6924 (m-10) cc_final: 0.6632 (m-10) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0661 time to fit residues: 5.6244 Evaluate side-chains 45 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.0470 chunk 50 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN A 197 HIS A 222 HIS A 386 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.168810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.137653 restraints weight = 4630.091| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.82 r_work: 0.3458 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4361 Z= 0.137 Angle : 0.760 12.657 5971 Z= 0.332 Chirality : 0.050 0.356 719 Planarity : 0.005 0.047 747 Dihedral : 13.509 87.343 859 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.64 % Allowed : 6.00 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.21 (0.38), residues: 519 helix: -1.51 (0.50), residues: 107 sheet: -3.11 (0.43), residues: 109 loop : -0.67 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 484 TYR 0.009 0.001 TYR A 445 PHE 0.017 0.001 PHE A 303 TRP 0.014 0.001 TRP A 166 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 4342) covalent geometry : angle 0.67264 / 0.31 ( 5918) SS BOND : bond 0.00133 / 0.07 ( 4) SS BOND : angle 1.33311 / 0.69 ( 8) hydrogen bonds : bond 0.04366 / 3.04 ( 101) hydrogen bonds : angle 5.67406 / 4.54 ( 195) link_BETA1-4 : bond 0.01103 / 0.57 ( 6) link_BETA1-4 : angle 4.96068 / 3.82 ( 18) link_BETA1-6 : bond 0.00975 / 0.51 ( 1) link_BETA1-6 : angle 3.04465 / 1.80 ( 3) link_NAG-ASN : bond 0.00508 / 0.34 ( 8) link_NAG-ASN : angle 3.47151 / 2.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.163 Fit side-chains REVERT: A 194 GLN cc_start: 0.7688 (mm110) cc_final: 0.7041 (mm-40) REVERT: A 321 MET cc_start: 0.8209 (mpp) cc_final: 0.7836 (mtt) REVERT: A 349 SER cc_start: 0.7260 (m) cc_final: 0.6761 (t) REVERT: A 469 ASP cc_start: 0.8004 (m-30) cc_final: 0.7770 (m-30) outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.0386 time to fit residues: 2.6759 Evaluate side-chains 44 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 336 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 0.0570 chunk 47 optimal weight: 0.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.163870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132938 restraints weight = 4658.148| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.71 r_work: 0.3435 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4361 Z= 0.142 Angle : 0.746 11.534 5971 Z= 0.325 Chirality : 0.049 0.371 719 Planarity : 0.004 0.043 747 Dihedral : 9.547 50.652 859 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.86 % Allowed : 7.28 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.13 (0.38), residues: 519 helix: -1.54 (0.51), residues: 107 sheet: -3.20 (0.44), residues: 102 loop : -0.60 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.010 0.001 TYR A 445 PHE 0.011 0.001 PHE A 303 TRP 0.013 0.001 TRP A 166 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 4342) covalent geometry : angle 0.66030 / 0.30 ( 5918) SS BOND : bond 0.00083 / 0.04 ( 4) SS BOND : angle 1.32973 / 0.67 ( 8) hydrogen bonds : bond 0.03951 / 2.75 ( 101) hydrogen bonds : angle 5.65555 / 4.49 ( 195) link_BETA1-4 : bond 0.01014 / 0.50 ( 6) link_BETA1-4 : angle 4.68201 / 3.63 ( 18) link_BETA1-6 : bond 0.00586 / 0.31 ( 1) link_BETA1-6 : angle 3.64796 / 2.10 ( 3) link_NAG-ASN : bond 0.00460 / 0.31 ( 8) link_NAG-ASN : angle 3.49809 / 2.01 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.159 Fit side-chains REVERT: A 190 ASP cc_start: 0.7483 (t0) cc_final: 0.7282 (t0) REVERT: A 194 GLN cc_start: 0.7770 (mm110) cc_final: 0.7131 (mm-40) REVERT: A 349 SER cc_start: 0.7281 (m) cc_final: 0.6789 (t) REVERT: A 469 ASP cc_start: 0.7921 (m-30) cc_final: 0.7661 (m-30) outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.0473 time to fit residues: 3.4658 Evaluate side-chains 43 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 336 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.0370 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.167177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136358 restraints weight = 4585.625| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.76 r_work: 0.3470 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4361 Z= 0.142 Angle : 0.724 10.306 5971 Z= 0.315 Chirality : 0.048 0.376 719 Planarity : 0.004 0.044 747 Dihedral : 8.227 42.665 859 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.86 % Allowed : 8.78 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.31 (0.38), residues: 519 helix: -1.70 (0.49), residues: 113 sheet: -3.28 (0.44), residues: 102 loop : -0.70 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 447 TYR 0.009 0.001 TYR A 445 PHE 0.017 0.001 PHE A 414 TRP 0.013 0.001 TRP A 166 HIS 0.002 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 4342) covalent geometry : angle 0.63808 / 0.29 ( 5918) SS BOND : bond 0.00083 / 0.04 ( 4) SS BOND : angle 1.19330 / 0.61 ( 8) hydrogen bonds : bond 0.03795 / 2.65 ( 101) hydrogen bonds : angle 5.59075 / 4.47 ( 195) link_BETA1-4 : bond 0.00946 / 0.48 ( 6) link_BETA1-4 : angle 4.30501 / 3.39 ( 18) link_BETA1-6 : bond 0.00333 / 0.18 ( 1) link_BETA1-6 : angle 3.21732 / 2.02 ( 3) link_NAG-ASN : bond 0.00571 / 0.35 ( 8) link_NAG-ASN : angle 3.79569 / 2.15 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.172 Fit side-chains REVERT: A 194 GLN cc_start: 0.7790 (mm110) cc_final: 0.7164 (mm-40) REVERT: A 198 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.6831 (m-80) REVERT: A 263 ASN cc_start: 0.7660 (t0) cc_final: 0.7357 (t0) REVERT: A 349 SER cc_start: 0.7294 (m) cc_final: 0.6790 (t) outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 0.0353 time to fit residues: 2.4398 Evaluate side-chains 42 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 289 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.0970 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.164959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.134228 restraints weight = 4630.103| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.76 r_work: 0.3441 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4361 Z= 0.133 Angle : 0.689 9.352 5971 Z= 0.304 Chirality : 0.048 0.361 719 Planarity : 0.004 0.044 747 Dihedral : 7.368 41.310 859 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.86 % Allowed : 10.28 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.13 (0.39), residues: 519 helix: -1.54 (0.52), residues: 107 sheet: -3.32 (0.44), residues: 102 loop : -0.55 (0.39), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 447 TYR 0.009 0.001 TYR A 445 PHE 0.017 0.001 PHE A 414 TRP 0.012 0.001 TRP A 166 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 4342) covalent geometry : angle 0.60878 / 0.28 ( 5918) SS BOND : bond 0.00083 / 0.04 ( 4) SS BOND : angle 1.17072 / 0.61 ( 8) hydrogen bonds : bond 0.03697 / 2.59 ( 101) hydrogen bonds : angle 5.56145 / 4.44 ( 195) link_BETA1-4 : bond 0.00970 / 0.50 ( 6) link_BETA1-4 : angle 4.07537 / 3.21 ( 18) link_BETA1-6 : bond 0.00339 / 0.18 ( 1) link_BETA1-6 : angle 2.79011 / 1.81 ( 3) link_NAG-ASN : bond 0.00441 / 0.31 ( 8) link_NAG-ASN : angle 3.57987 / 2.10 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.178 Fit side-chains REVERT: A 194 GLN cc_start: 0.7836 (mm110) cc_final: 0.7220 (mm-40) REVERT: A 198 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.6924 (m-80) REVERT: A 263 ASN cc_start: 0.7619 (t0) cc_final: 0.7293 (t0) REVERT: A 349 SER cc_start: 0.7297 (m) cc_final: 0.6799 (t) outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 0.0503 time to fit residues: 3.5238 Evaluate side-chains 45 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 359 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.175598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.144680 restraints weight = 4552.234| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.81 r_work: 0.3452 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4361 Z= 0.122 Angle : 0.667 8.816 5971 Z= 0.296 Chirality : 0.047 0.349 719 Planarity : 0.004 0.045 747 Dihedral : 6.862 40.935 859 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.07 % Allowed : 11.35 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.39), residues: 519 helix: -1.45 (0.52), residues: 106 sheet: -3.31 (0.44), residues: 102 loop : -0.53 (0.39), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 447 TYR 0.009 0.001 TYR A 445 PHE 0.018 0.001 PHE A 414 TRP 0.012 0.001 TRP A 166 HIS 0.001 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 4342) covalent geometry : angle 0.59349 / 0.28 ( 5918) SS BOND : bond 0.00077 / 0.04 ( 4) SS BOND : angle 1.06968 / 0.56 ( 8) hydrogen bonds : bond 0.03694 / 2.58 ( 101) hydrogen bonds : angle 5.45968 / 4.38 ( 195) link_BETA1-4 : bond 0.00934 / 0.48 ( 6) link_BETA1-4 : angle 3.96734 / 3.15 ( 18) link_BETA1-6 : bond 0.00324 / 0.17 ( 1) link_BETA1-6 : angle 2.47690 / 1.74 ( 3) link_NAG-ASN : bond 0.00467 / 0.33 ( 8) link_NAG-ASN : angle 3.28530 / 1.90 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7807 (mm110) cc_final: 0.7185 (mm-40) REVERT: A 198 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.6798 (m-80) REVERT: A 263 ASN cc_start: 0.7589 (t0) cc_final: 0.7216 (t0) REVERT: A 349 SER cc_start: 0.7269 (m) cc_final: 0.6760 (t) outliers start: 5 outliers final: 2 residues processed: 48 average time/residue: 0.0482 time to fit residues: 3.4052 Evaluate side-chains 46 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 289 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.161325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130724 restraints weight = 4749.238| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.73 r_work: 0.3461 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4361 Z= 0.149 Angle : 0.692 8.428 5971 Z= 0.311 Chirality : 0.048 0.374 719 Planarity : 0.004 0.044 747 Dihedral : 6.861 41.775 859 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.50 % Allowed : 11.56 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.39), residues: 519 helix: -1.66 (0.50), residues: 112 sheet: -3.35 (0.44), residues: 102 loop : -0.63 (0.39), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 447 TYR 0.008 0.001 TYR A 445 PHE 0.017 0.001 PHE A 414 TRP 0.009 0.001 TRP A 166 HIS 0.002 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 4342) covalent geometry : angle 0.62369 / 0.29 ( 5918) SS BOND : bond 0.00072 / 0.04 ( 4) SS BOND : angle 1.17922 / 0.62 ( 8) hydrogen bonds : bond 0.03868 / 2.70 ( 101) hydrogen bonds : angle 5.57857 / 4.46 ( 195) link_BETA1-4 : bond 0.00882 / 0.44 ( 6) link_BETA1-4 : angle 3.92435 / 3.11 ( 18) link_BETA1-6 : bond 0.00339 / 0.18 ( 1) link_BETA1-6 : angle 2.23393 / 1.62 ( 3) link_NAG-ASN : bond 0.00389 / 0.26 ( 8) link_NAG-ASN : angle 3.24749 / 1.87 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.187 Fit side-chains REVERT: A 194 GLN cc_start: 0.7848 (mm110) cc_final: 0.7252 (mm-40) REVERT: A 198 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.6961 (m-80) REVERT: A 263 ASN cc_start: 0.7683 (t0) cc_final: 0.7290 (t0) REVERT: A 349 SER cc_start: 0.7392 (m) cc_final: 0.6889 (t) REVERT: A 389 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7466 (mp) outliers start: 7 outliers final: 4 residues processed: 47 average time/residue: 0.0478 time to fit residues: 3.3285 Evaluate side-chains 47 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 410 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.185503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.156412 restraints weight = 4345.274| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.45 r_work: 0.3505 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4361 Z= 0.109 Angle : 0.642 8.515 5971 Z= 0.288 Chirality : 0.046 0.316 719 Planarity : 0.004 0.046 747 Dihedral : 6.363 40.226 859 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.07 % Allowed : 11.99 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.39), residues: 519 helix: -1.43 (0.53), residues: 106 sheet: -3.31 (0.44), residues: 102 loop : -0.48 (0.39), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.010 0.001 TYR A 445 PHE 0.018 0.001 PHE A 414 TRP 0.013 0.001 TRP A 166 HIS 0.001 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 4342) covalent geometry : angle 0.57513 / 0.27 ( 5918) SS BOND : bond 0.00079 / 0.04 ( 4) SS BOND : angle 0.92961 / 0.48 ( 8) hydrogen bonds : bond 0.03486 / 2.45 ( 101) hydrogen bonds : angle 5.39445 / 4.32 ( 195) link_BETA1-4 : bond 0.00987 / 0.51 ( 6) link_BETA1-4 : angle 3.68434 / 2.96 ( 18) link_BETA1-6 : bond 0.00376 / 0.20 ( 1) link_BETA1-6 : angle 1.97329 / 1.49 ( 3) link_NAG-ASN : bond 0.00467 / 0.34 ( 8) link_NAG-ASN : angle 3.15070 / 1.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.097 Fit side-chains REVERT: A 194 GLN cc_start: 0.7963 (mm110) cc_final: 0.7392 (mm-40) REVERT: A 198 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7018 (m-80) REVERT: A 263 ASN cc_start: 0.7830 (t0) cc_final: 0.7435 (t0) REVERT: A 349 SER cc_start: 0.7453 (m) cc_final: 0.6985 (t) REVERT: A 389 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7792 (mp) outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.0457 time to fit residues: 3.3163 Evaluate side-chains 51 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 410 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 42 optimal weight: 0.1980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.183666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.153980 restraints weight = 4411.249| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.53 r_work: 0.3488 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4361 Z= 0.123 Angle : 0.653 8.245 5971 Z= 0.294 Chirality : 0.046 0.338 719 Planarity : 0.004 0.045 747 Dihedral : 6.311 40.671 859 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.28 % Allowed : 11.35 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.38), residues: 519 helix: -1.59 (0.50), residues: 112 sheet: -3.32 (0.44), residues: 103 loop : -0.56 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 447 TYR 0.009 0.001 TYR A 445 PHE 0.020 0.001 PHE A 414 TRP 0.012 0.001 TRP A 57 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 4342) covalent geometry : angle 0.58800 / 0.28 ( 5918) SS BOND : bond 0.00083 / 0.04 ( 4) SS BOND : angle 1.04777 / 0.55 ( 8) hydrogen bonds : bond 0.03691 / 2.59 ( 101) hydrogen bonds : angle 5.38275 / 4.28 ( 195) link_BETA1-4 : bond 0.00941 / 0.47 ( 6) link_BETA1-4 : angle 3.70543 / 2.96 ( 18) link_BETA1-6 : bond 0.00397 / 0.21 ( 1) link_BETA1-6 : angle 1.84765 / 1.41 ( 3) link_NAG-ASN : bond 0.00375 / 0.27 ( 8) link_NAG-ASN : angle 3.10435 / 1.81 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7992 (mm110) cc_final: 0.7431 (mm-40) REVERT: A 198 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7059 (m-80) REVERT: A 349 SER cc_start: 0.7559 (m) cc_final: 0.7091 (t) REVERT: A 389 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7820 (mp) outliers start: 6 outliers final: 3 residues processed: 48 average time/residue: 0.0485 time to fit residues: 3.4092 Evaluate side-chains 48 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 410 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 0.0170 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN A 510 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.178630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146832 restraints weight = 4457.550| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.86 r_work: 0.3474 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4361 Z= 0.112 Angle : 0.638 8.367 5971 Z= 0.287 Chirality : 0.045 0.315 719 Planarity : 0.004 0.045 747 Dihedral : 6.134 40.242 859 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.07 % Allowed : 11.56 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.39), residues: 519 helix: -1.39 (0.53), residues: 106 sheet: -3.30 (0.44), residues: 103 loop : -0.41 (0.39), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.009 0.001 TYR A 445 PHE 0.019 0.001 PHE A 414 TRP 0.016 0.002 TRP A 57 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 4342) covalent geometry : angle 0.57440 / 0.27 ( 5918) SS BOND : bond 0.00090 / 0.05 ( 4) SS BOND : angle 1.00386 / 0.53 ( 8) hydrogen bonds : bond 0.03561 / 2.51 ( 101) hydrogen bonds : angle 5.32563 / 4.25 ( 195) link_BETA1-4 : bond 0.00959 / 0.49 ( 6) link_BETA1-4 : angle 3.61292 / 2.91 ( 18) link_BETA1-6 : bond 0.00408 / 0.21 ( 1) link_BETA1-6 : angle 1.74368 / 1.35 ( 3) link_NAG-ASN : bond 0.00417 / 0.30 ( 8) link_NAG-ASN : angle 3.07454 / 1.81 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1038 Ramachandran restraints generated. 519 Oldfield, 0 Emsley, 519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7751 (mm110) cc_final: 0.7168 (mm-40) REVERT: A 198 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: A 349 SER cc_start: 0.7251 (m) cc_final: 0.6730 (t) REVERT: A 389 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7428 (mp) outliers start: 5 outliers final: 3 residues processed: 48 average time/residue: 0.0464 time to fit residues: 3.3132 Evaluate side-chains 49 residues out of total 467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 410 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.173048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.141214 restraints weight = 4526.711| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.87 r_work: 0.3428 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4361 Z= 0.121 Angle : 0.645 8.233 5971 Z= 0.291 Chirality : 0.046 0.326 719 Planarity : 0.004 0.045 747 Dihedral : 6.129 40.330 859 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.07 % Allowed : 11.99 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.39), residues: 519 helix: -1.57 (0.50), residues: 112 sheet: -3.26 (0.45), residues: 102 loop : -0.51 (0.39), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.009 0.001 TYR A 445 PHE 0.019 0.001 PHE A 414 TRP 0.015 0.001 TRP A 57 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 ( 4342) covalent geometry : angle 0.58205 / 0.28 ( 5918) SS BOND : bond 0.00079 / 0.04 ( 4) SS BOND : angle 1.02058 / 0.53 ( 8) hydrogen bonds : bond 0.03652 / 2.56 ( 101) hydrogen bonds : angle 5.34585 / 4.27 ( 195) link_BETA1-4 : bond 0.00933 / 0.47 ( 6) link_BETA1-4 : angle 3.62130 / 2.91 ( 18) link_BETA1-6 : bond 0.00421 / 0.22 ( 1) link_BETA1-6 : angle 1.70474 / 1.33 ( 3) link_NAG-ASN : bond 0.00384 / 0.27 ( 8) link_NAG-ASN : angle 3.08392 / 1.80 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1135.99 seconds wall clock time: 20 minutes 10.75 seconds (1210.75 seconds total)