Starting phenix.real_space_refine on Thu Jul 2 07:07:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7drt_30827/07_2026/7drt_30827.cif Found real_map, /net/cci-nas-00/data/ceres_data/7drt_30827/07_2026/7drt_30827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7drt_30827/07_2026/7drt_30827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7drt_30827/07_2026/7drt_30827.map" model { file = "/net/cci-nas-00/data/ceres_data/7drt_30827/07_2026/7drt_30827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7drt_30827/07_2026/7drt_30827.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7drt_30827/07_2026/7drt_30827.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7drt_30827/07_2026/7drt_30827.cif" } resolution = 2.2 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= 0.057 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 P 3 5.49 5 S 66 5.16 5 C 4438 2.51 5 N 1152 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 6849 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2618 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 15, 'TRANS': 318} Chain: "B" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4037 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 21, 'TRANS': 474} Chain: "H" 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 chiralities: 2 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'PAM': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'PAM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'CLR': 1, 'LPE': 1, 'PCW': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 1.42, per 1000 atoms: 0.21 Number of scatterers: 6849 At special positions: 0 Unit cell: (123.918, 91.308, 96.1995, 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) S 66 16.00 P 3 15.00 O 1190 8.00 N 1152 7.00 C 4438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 56 " distance=2.07 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=1.79 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 155 " distance=2.15 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 217 " distance=2.07 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 312 " distance=2.07 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 307 " distance=2.09 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 351 " distance=2.09 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 342 " distance=2.04 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 339 " distance=2.01 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 335 " distance=2.34 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 71 " distance=2.02 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 179 " distance=2.07 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=1, symmetry=0 Links applied BETA1-4 " NAG H 1 " - " NAG H 2 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 308.1 milliseconds 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1540 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 7 sheets defined 47.3% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 removed outlier: 5.968A pdb=" N GLY A 29 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Proline residue: A 30 - end of helix Processing helix chain 'A' and resid 49 through 59 Processing helix chain 'A' and resid 62 through 81 removed outlier: 3.613A pdb=" N VAL A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 67 " --> pdb=" O MET A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.650A pdb=" N LEU A 102 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS A 104 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 130 Processing helix chain 'A' and resid 160 through 170 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 178 through 198 Processing helix chain 'A' and resid 223 through 238 removed outlier: 3.618A pdb=" N ILE A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 removed outlier: 3.994A pdb=" N CYS A 311 " --> pdb=" O CYS A 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 10 through 35 removed outlier: 3.507A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 204 through 208 removed outlier: 3.571A pdb=" N LYS B 208 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 258 Proline residue: B 243 - end of helix Processing helix chain 'B' and resid 264 through 282 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 295 through 322 Processing helix chain 'B' and resid 331 through 334 removed outlier: 4.036A pdb=" N GLY B 334 " --> pdb=" O HIS B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 331 through 334' Processing helix chain 'B' and resid 335 through 363 Proline residue: B 341 - end of helix removed outlier: 3.704A pdb=" N THR B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 411 Processing helix chain 'B' and resid 418 through 455 Processing helix chain 'B' and resid 469 through 492 removed outlier: 3.558A pdb=" N ASN B 482 " --> pdb=" O TYR B 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 206 Processing sheet with id=AA2, first strand: chain 'A' and resid 253 through 258 Processing sheet with id=AA3, first strand: chain 'A' and resid 319 through 327 removed outlier: 3.761A pdb=" N GLN A 340 " --> pdb=" O CYS A 327 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 46 removed outlier: 3.995A pdb=" N GLU B 215 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP B 117 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ILE B 219 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN B 115 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 221 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 113 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY B 223 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 111 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU B 114 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 74 removed outlier: 4.495A pdb=" N LYS B 49 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 132 " --> pdb=" O PRO B 157 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N MET B 134 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ARG B 155 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 136 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N HIS B 153 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 138 " --> pdb=" O MET B 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 162 through 163 Processing sheet with id=AA7, first strand: chain 'B' and resid 459 through 462 351 hydrogen bonds defined for protein. 981 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: 0.98 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1050 1.29 - 1.43: 1958 1.43 - 1.56: 3916 1.56 - 1.69: 10 1.69 - 1.82: 96 Bond restraints: 7030 Sorted by residual: bond pdb=" C TRP A 86 " pdb=" N ASN A 87 " ideal model delta sigma weight residual 1.332 1.446 -0.114 1.34e-02 5.57e+03 7.23e+01 bond pdb=" C11 PCW A 502 " pdb=" O3 PCW A 502 " ideal model delta sigma weight residual 1.326 1.458 -0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" C GLU B 205 " pdb=" N LYS B 206 " ideal model delta sigma weight residual 1.332 1.232 0.100 1.53e-02 4.27e+03 4.30e+01 bond pdb=" C31 PCW A 502 " pdb=" O2 PCW A 502 " ideal model delta sigma weight residual 1.333 1.450 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" C PHE B 246 " pdb=" N ILE B 247 " ideal model delta sigma weight residual 1.334 1.261 0.073 1.26e-02 6.30e+03 3.37e+01 ... (remaining 7025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 8985 2.65 - 5.30: 429 5.30 - 7.96: 63 7.96 - 10.61: 15 10.61 - 13.26: 5 Bond angle restraints: 9497 Sorted by residual: angle pdb=" N SER A 301 " pdb=" CA SER A 301 " pdb=" C SER A 301 " ideal model delta sigma weight residual 113.38 102.61 10.77 1.23e+00 6.61e-01 7.67e+01 angle pdb=" N PHE A 331 " pdb=" CA PHE A 331 " pdb=" C PHE A 331 " ideal model delta sigma weight residual 111.28 122.43 -11.15 1.35e+00 5.49e-01 6.82e+01 angle pdb=" C ARG A 269 " pdb=" N ASP A 270 " pdb=" CA ASP A 270 " ideal model delta sigma weight residual 123.01 109.75 13.26 1.78e+00 3.16e-01 5.55e+01 angle pdb=" N ASN B 330 " pdb=" CA ASN B 330 " pdb=" C ASN B 330 " ideal model delta sigma weight residual 110.44 118.03 -7.59 1.20e+00 6.94e-01 4.00e+01 angle pdb=" N VAL B 455 " pdb=" CA VAL B 455 " pdb=" C VAL B 455 " ideal model delta sigma weight residual 113.43 120.31 -6.88 1.09e+00 8.42e-01 3.99e+01 ... (remaining 9492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.43: 4000 28.43 - 56.86: 118 56.86 - 85.30: 22 85.30 - 113.73: 1 113.73 - 142.16: 1 Dihedral angle restraints: 4142 sinusoidal: 1750 harmonic: 2392 Sorted by residual: dihedral pdb=" CB CYS A 327 " pdb=" SG CYS A 327 " pdb=" SG CYS A 342 " pdb=" CB CYS A 342 " ideal model delta sinusoidal sigma weight residual 93.00 170.47 -77.47 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" C PHE B 395 " pdb=" N PHE B 395 " pdb=" CA PHE B 395 " pdb=" CB PHE B 395 " ideal model delta harmonic sigma weight residual -122.60 -141.74 19.14 0 2.50e+00 1.60e-01 5.86e+01 dihedral pdb=" N PHE B 395 " pdb=" C PHE B 395 " pdb=" CA PHE B 395 " pdb=" CB PHE B 395 " ideal model delta harmonic sigma weight residual 122.80 141.75 -18.95 0 2.50e+00 1.60e-01 5.74e+01 ... (remaining 4139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 956 0.158 - 0.315: 34 0.315 - 0.473: 8 0.473 - 0.630: 3 0.630 - 0.788: 2 Chirality restraints: 1003 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.35e+02 chirality pdb=" CA PHE B 395 " pdb=" N PHE B 395 " pdb=" C PHE B 395 " pdb=" CB PHE B 395 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.55e+01 chirality pdb=" CA VAL A 91 " pdb=" N VAL A 91 " pdb=" C VAL A 91 " pdb=" CB VAL A 91 " both_signs ideal model delta sigma weight residual False 2.44 1.77 0.67 2.00e-01 2.50e+01 1.12e+01 ... (remaining 1000 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.339 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG H 1 " -0.096 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.202 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.484 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PAM A 501 " 0.074 2.00e-02 2.50e+03 5.67e-02 3.21e+01 pdb=" C11 PAM A 501 " -0.031 2.00e-02 2.50e+03 pdb=" C8 PAM A 501 " 0.031 2.00e-02 2.50e+03 pdb=" C9 PAM A 501 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 205 " 0.024 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C GLU B 205 " -0.086 2.00e-02 2.50e+03 pdb=" O GLU B 205 " 0.031 2.00e-02 2.50e+03 pdb=" N LYS B 206 " 0.031 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 54 2.63 - 3.20: 5929 3.20 - 3.77: 9728 3.77 - 4.33: 14025 4.33 - 4.90: 22690 Nonbonded interactions: 52426 Sorted by model distance: nonbonded pdb=" ND2 ASN A 87 " pdb=" C1 NAG H 1 " model vdw 2.064 3.550 nonbonded pdb=" ND2 ASN A 87 " pdb=" O5 NAG H 1 " model vdw 2.279 3.120 nonbonded pdb=" OE2 GLU A 108 " pdb=" O HOH A 601 " model vdw 2.335 3.040 nonbonded pdb=" O HIS A 142 " pdb=" CG GLN A 143 " model vdw 2.366 3.440 nonbonded pdb=" OE2 GLU B 79 " pdb=" O HOH B 701 " model vdw 2.372 3.040 ... (remaining 52421 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 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: 11.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.190 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 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 : 0.012 0.310 7046 Z= 0.750 Angle : 1.338 13.262 9528 Z= 0.845 Chirality : 0.089 0.788 1003 Planarity : 0.011 0.283 1184 Dihedral : 12.979 142.161 2560 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.45 % Favored : 94.07 % Rotamer: Outliers : 2.38 % Allowed : 1.40 % Favored : 96.22 % Cbeta Deviations : 1.17 % 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: -0.76 (0.27), residues: 826 helix: 0.39 (0.25), residues: 361 sheet: 0.91 (0.44), residues: 112 loop : -1.97 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 303 TYR 0.011 0.000 TYR A 260 PHE 0.015 0.001 PHE B 486 TRP 0.029 0.002 TRP B 295 HIS 0.003 0.000 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.01100 / 0.67 ( 7030) covalent geometry : angle 1.32563 / 0.84 ( 9497) SS BOND : bond 0.11354 / 5.55 ( 14) SS BOND : angle 3.39126 / 1.93 ( 28) hydrogen bonds : bond 0.20923 / 13.31 ( 351) hydrogen bonds : angle 6.66016 / 4.73 ( 981) Misc. bond : bond 0.17773 / 9.35 ( 1) link_BETA1-4 : bond 0.02367 / 1.25 ( 1) link_BETA1-4 : angle 4.13002 / 2.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 266 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.4398 (tttt) cc_final: 0.4161 (ttpp) REVERT: A 76 GLU cc_start: 0.5498 (tp30) cc_final: 0.5144 (tp30) REVERT: A 85 ARG cc_start: 0.4342 (mtt180) cc_final: 0.4121 (mtt-85) REVERT: A 89 THR cc_start: 0.5757 (t) cc_final: 0.5528 (p) REVERT: A 106 THR cc_start: 0.4441 (p) cc_final: 0.4007 (t) REVERT: A 107 ARG cc_start: 0.4923 (mtm-85) cc_final: 0.4260 (mtp-110) REVERT: A 109 SER cc_start: 0.5964 (m) cc_final: 0.5451 (p) REVERT: A 168 GLU cc_start: 0.4676 (tp30) cc_final: 0.4458 (mm-30) REVERT: A 175 ASN cc_start: 0.5281 (m-40) cc_final: 0.5075 (m110) REVERT: A 188 ASN cc_start: 0.6683 (m-40) cc_final: 0.6449 (m-40) REVERT: A 189 GLU cc_start: 0.5369 (tp30) cc_final: 0.4939 (tp30) REVERT: A 193 GLN cc_start: 0.5761 (mm-40) cc_final: 0.5273 (mm110) REVERT: A 200 HIS cc_start: 0.6542 (m-70) cc_final: 0.6319 (m90) REVERT: A 229 ASP cc_start: 0.5451 (m-30) cc_final: 0.4661 (t70) REVERT: A 231 LEU cc_start: 0.5883 (mt) cc_final: 0.5663 (mm) REVERT: A 236 ASP cc_start: 0.4946 (m-30) cc_final: 0.4549 (m-30) REVERT: A 277 SER cc_start: 0.5319 (m) cc_final: 0.4989 (t) REVERT: B 11 THR cc_start: 0.4905 (p) cc_final: 0.4582 (t) REVERT: B 20 ILE cc_start: 0.7041 (mt) cc_final: 0.6669 (mm) REVERT: B 21 LEU cc_start: 0.6420 (mt) cc_final: 0.6171 (mp) REVERT: B 22 LEU cc_start: 0.6108 (tp) cc_final: 0.5833 (tm) REVERT: B 69 ASN cc_start: 0.6332 (m-40) cc_final: 0.6089 (m-40) REVERT: B 79 GLU cc_start: 0.5426 (mt-10) cc_final: 0.5096 (mt-10) REVERT: B 84 GLU cc_start: 0.5758 (mt-10) cc_final: 0.4497 (tm-30) REVERT: B 86 GLU cc_start: 0.5020 (mt-10) cc_final: 0.4500 (mp0) REVERT: B 104 SER cc_start: 0.7808 (p) cc_final: 0.7488 (t) REVERT: B 117 ASP cc_start: 0.7171 (m-30) cc_final: 0.6936 (m-30) REVERT: B 125 GLN cc_start: 0.5379 (mt0) cc_final: 0.4427 (mp10) REVERT: B 154 GLU cc_start: 0.6207 (mm-30) cc_final: 0.5956 (mm-30) REVERT: B 171 GLU cc_start: 0.5472 (mt-10) cc_final: 0.4947 (pm20) REVERT: B 178 GLU cc_start: 0.6346 (mt-10) cc_final: 0.6029 (mt-10) REVERT: B 215 GLU cc_start: 0.6183 (tt0) cc_final: 0.5873 (mm-30) REVERT: B 259 MET cc_start: 0.5725 (mmm) cc_final: 0.4736 (mmm) REVERT: B 261 ARG cc_start: 0.5861 (ptt-90) cc_final: 0.5583 (ptt-90) REVERT: B 267 GLU cc_start: 0.6211 (mt-10) cc_final: 0.4949 (pp20) REVERT: B 276 SER cc_start: 0.7258 (m) cc_final: 0.6739 (p) REVERT: B 316 ILE cc_start: 0.5627 (mm) cc_final: 0.5193 (mt) REVERT: B 370 THR cc_start: 0.6023 (m) cc_final: 0.5654 (p) REVERT: B 421 ARG cc_start: 0.3800 (mtm180) cc_final: 0.3201 (mmp-170) REVERT: B 422 ARG cc_start: 0.4831 (ttt180) cc_final: 0.4620 (ttp80) REVERT: B 482 ASN cc_start: 0.5894 (m-40) cc_final: 0.5664 (m-40) REVERT: B 483 LEU cc_start: 0.6842 (tp) cc_final: 0.6527 (mt) REVERT: B 495 SER cc_start: 0.6552 (t) cc_final: 0.6285 (p) REVERT: B 497 LYS cc_start: 0.6239 (mttt) cc_final: 0.5983 (mmtt) outliers start: 17 outliers final: 7 residues processed: 276 average time/residue: 0.4070 time to fit residues: 118.5763 Evaluate side-chains 184 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 177 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 452 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 78 GLN A 184 ASN A 186 HIS A 279 ASN B 70 HIS B 95 HIS B 406 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.245905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.227984 restraints weight = 6186.176| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 1.15 r_work: 0.4356 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.4259 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7046 Z= 0.136 Angle : 0.576 7.741 9528 Z= 0.309 Chirality : 0.043 0.141 1003 Planarity : 0.005 0.039 1184 Dihedral : 9.832 114.118 1016 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.39 % Favored : 96.37 % Rotamer: Outliers : 5.87 % Allowed : 12.31 % Favored : 81.82 % 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: 0.91 (0.30), residues: 826 helix: 2.51 (0.27), residues: 354 sheet: 0.70 (0.42), residues: 137 loop : -1.66 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 254 TYR 0.017 0.002 TYR A 274 PHE 0.022 0.002 PHE B 401 TRP 0.018 0.001 TRP B 481 HIS 0.007 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 ( 7030) covalent geometry : angle 0.57455 / 0.31 ( 9497) SS BOND : bond 0.00274 / 0.14 ( 14) SS BOND : angle 0.84735 / 0.53 ( 28) hydrogen bonds : bond 0.06263 / 4.07 ( 351) hydrogen bonds : angle 4.45854 / 3.21 ( 981) Misc. bond : bond 0.00053 / 0.03 ( 1) link_BETA1-4 : bond 0.00043 / 0.02 ( 1) link_BETA1-4 : angle 1.64415 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 240 GLU cc_start: 0.7719 (tt0) cc_final: 0.6789 (tm-30) outliers start: 42 outliers final: 22 residues processed: 205 average time/residue: 0.4783 time to fit residues: 103.5706 Evaluate side-chains 165 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 0 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 78 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN A 246 HIS B 8 ASN B 70 HIS B 225 HIS B 411 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.231832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.212077 restraints weight = 5841.374| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 1.05 r_work: 0.4190 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.4098 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7046 Z= 0.215 Angle : 0.674 7.562 9528 Z= 0.368 Chirality : 0.047 0.149 1003 Planarity : 0.006 0.056 1184 Dihedral : 9.259 101.573 1007 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.33 % Favored : 94.55 % Rotamer: Outliers : 8.11 % Allowed : 15.38 % Favored : 76.50 % 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: 0.08 (0.29), residues: 826 helix: 2.09 (0.27), residues: 347 sheet: 0.24 (0.45), residues: 134 loop : -2.32 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 254 TYR 0.021 0.002 TYR A 274 PHE 0.038 0.002 PHE B 401 TRP 0.025 0.002 TRP B 336 HIS 0.019 0.002 HIS B 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 ( 7030) covalent geometry : angle 0.67108 / 0.37 ( 9497) SS BOND : bond 0.00513 / 0.28 ( 14) SS BOND : angle 1.15187 / 0.72 ( 28) hydrogen bonds : bond 0.08135 / 5.23 ( 351) hydrogen bonds : angle 4.92378 / 3.56 ( 981) Misc. bond : bond 0.00008 / 0.00 ( 1) link_BETA1-4 : bond 0.00436 / 0.23 ( 1) link_BETA1-4 : angle 1.70493 / 0.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 153 time to evaluate : 0.277 Fit side-chains REVERT: A 71 LYS cc_start: 0.7684 (tttt) cc_final: 0.7484 (ttpp) REVERT: A 84 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7497 (mtt90) REVERT: A 126 ARG cc_start: 0.8057 (ttt-90) cc_final: 0.7845 (ttt-90) REVERT: A 232 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7399 (tmmt) REVERT: A 286 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6566 (tm-30) REVERT: B 125 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6712 (pm20) REVERT: B 255 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7769 (tpt90) outliers start: 58 outliers final: 36 residues processed: 196 average time/residue: 0.4013 time to fit residues: 83.9519 Evaluate side-chains 195 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 12 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 40 optimal weight: 0.0570 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 78 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN B 70 HIS B 331 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.232564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.212859 restraints weight = 5888.533| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 1.06 r_work: 0.4216 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.4126 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7046 Z= 0.184 Angle : 0.638 8.123 9528 Z= 0.346 Chirality : 0.045 0.156 1003 Planarity : 0.006 0.053 1184 Dihedral : 8.994 87.430 1007 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.21 % Favored : 94.67 % Rotamer: Outliers : 8.25 % Allowed : 18.60 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.10 (0.29), residues: 826 helix: 2.07 (0.27), residues: 347 sheet: 0.01 (0.47), residues: 131 loop : -2.49 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 405 TYR 0.025 0.002 TYR A 274 PHE 0.032 0.002 PHE B 401 TRP 0.024 0.002 TRP B 336 HIS 0.008 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 7030) covalent geometry : angle 0.63421 / 0.34 ( 9497) SS BOND : bond 0.00382 / 0.23 ( 14) SS BOND : angle 1.27359 / 0.74 ( 28) hydrogen bonds : bond 0.07353 / 4.74 ( 351) hydrogen bonds : angle 4.79671 / 3.47 ( 981) Misc. bond : bond 0.00047 / 0.02 ( 1) link_BETA1-4 : bond 0.00343 / 0.18 ( 1) link_BETA1-4 : angle 1.95229 / 1.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 147 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7423 (mtt90) REVERT: A 126 ARG cc_start: 0.8142 (ttt-90) cc_final: 0.7918 (ttt-90) REVERT: A 232 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7352 (tmmt) REVERT: A 286 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6622 (tm-30) REVERT: B 255 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7727 (tpt90) outliers start: 59 outliers final: 38 residues processed: 183 average time/residue: 0.3985 time to fit residues: 77.6656 Evaluate side-chains 183 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 62 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 78 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN B 70 HIS B 331 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.231455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.211677 restraints weight = 5864.882| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 1.08 r_work: 0.4191 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.4102 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7046 Z= 0.184 Angle : 0.640 9.295 9528 Z= 0.347 Chirality : 0.045 0.156 1003 Planarity : 0.005 0.054 1184 Dihedral : 8.769 75.653 1007 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.45 % Favored : 94.43 % Rotamer: Outliers : 7.97 % Allowed : 19.72 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.29), residues: 826 helix: 1.98 (0.27), residues: 347 sheet: -0.27 (0.46), residues: 131 loop : -2.58 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 225 TYR 0.027 0.002 TYR A 274 PHE 0.029 0.002 PHE B 401 TRP 0.024 0.002 TRP B 336 HIS 0.007 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 7030) covalent geometry : angle 0.63607 / 0.35 ( 9497) SS BOND : bond 0.00406 / 0.26 ( 14) SS BOND : angle 1.23727 / 0.72 ( 28) hydrogen bonds : bond 0.07343 / 4.73 ( 351) hydrogen bonds : angle 4.83831 / 3.50 ( 981) Misc. bond : bond 0.00032 / 0.02 ( 1) link_BETA1-4 : bond 0.00016 / 0.01 ( 1) link_BETA1-4 : angle 2.00989 / 1.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 145 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.8142 (ttt-90) cc_final: 0.7919 (ttt-90) REVERT: A 173 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.5994 (tmm160) REVERT: A 232 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7338 (tmmt) REVERT: A 286 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6731 (tm-30) REVERT: A 292 THR cc_start: 0.5550 (p) cc_final: 0.4931 (t) REVERT: B 11 THR cc_start: 0.5243 (OUTLIER) cc_final: 0.4004 (t) REVERT: B 218 ASP cc_start: 0.7315 (m-30) cc_final: 0.7075 (m-30) REVERT: B 255 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7739 (tpt90) outliers start: 57 outliers final: 42 residues processed: 184 average time/residue: 0.4129 time to fit residues: 81.1276 Evaluate side-chains 191 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 78 GLN A 87 ASN A 193 GLN B 70 HIS B 331 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.234177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.214942 restraints weight = 5917.703| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 1.07 r_work: 0.4220 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.4128 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7046 Z= 0.156 Angle : 0.612 9.794 9528 Z= 0.327 Chirality : 0.044 0.155 1003 Planarity : 0.005 0.052 1184 Dihedral : 8.264 68.882 1007 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.33 % Favored : 94.55 % Rotamer: Outliers : 7.83 % Allowed : 20.84 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.30), residues: 826 helix: 2.04 (0.27), residues: 354 sheet: -0.25 (0.46), residues: 130 loop : -2.57 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 405 TYR 0.022 0.002 TYR A 274 PHE 0.022 0.002 PHE B 401 TRP 0.022 0.001 TRP B 336 HIS 0.006 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 7030) covalent geometry : angle 0.60895 / 0.33 ( 9497) SS BOND : bond 0.00368 / 0.23 ( 14) SS BOND : angle 1.08706 / 0.64 ( 28) hydrogen bonds : bond 0.06630 / 4.28 ( 351) hydrogen bonds : angle 4.66935 / 3.37 ( 981) Misc. bond : bond 0.00035 / 0.02 ( 1) link_BETA1-4 : bond 0.00002 / 0.00 ( 1) link_BETA1-4 : angle 1.86577 / 0.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 149 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7448 (mtt90) REVERT: A 126 ARG cc_start: 0.8117 (ttt-90) cc_final: 0.7899 (ttt-90) REVERT: A 173 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.5941 (tmm160) REVERT: A 232 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7298 (tmmt) REVERT: A 268 GLU cc_start: 0.6925 (mp0) cc_final: 0.6658 (mp0) REVERT: A 269 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6509 (ttm170) REVERT: A 286 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6721 (tm-30) REVERT: A 292 THR cc_start: 0.5390 (p) cc_final: 0.4798 (t) REVERT: B 11 THR cc_start: 0.4917 (OUTLIER) cc_final: 0.3573 (m) REVERT: B 218 ASP cc_start: 0.7298 (m-30) cc_final: 0.7086 (m-30) REVERT: B 255 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7680 (tpt90) REVERT: B 497 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6821 (mmtt) outliers start: 56 outliers final: 35 residues processed: 188 average time/residue: 0.4634 time to fit residues: 92.4995 Evaluate side-chains 183 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 64 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 78 GLN A 87 ASN A 193 GLN B 70 HIS B 331 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.234644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.215123 restraints weight = 5900.988| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 1.09 r_work: 0.4238 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.4139 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7046 Z= 0.143 Angle : 0.596 10.796 9528 Z= 0.318 Chirality : 0.043 0.154 1003 Planarity : 0.005 0.050 1184 Dihedral : 7.913 64.562 1005 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.33 % Favored : 94.55 % Rotamer: Outliers : 7.55 % Allowed : 22.10 % Favored : 70.35 % 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: -0.15 (0.30), residues: 826 helix: 2.13 (0.27), residues: 354 sheet: -0.42 (0.45), residues: 133 loop : -2.55 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 185 TYR 0.020 0.002 TYR A 274 PHE 0.019 0.001 PHE B 401 TRP 0.021 0.001 TRP B 336 HIS 0.006 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 7030) covalent geometry : angle 0.59393 / 0.32 ( 9497) SS BOND : bond 0.00322 / 0.20 ( 14) SS BOND : angle 1.03485 / 0.61 ( 28) hydrogen bonds : bond 0.06312 / 4.09 ( 351) hydrogen bonds : angle 4.59474 / 3.31 ( 981) Misc. bond : bond 0.00028 / 0.01 ( 1) link_BETA1-4 : bond 0.00000 / 0.00 ( 1) link_BETA1-4 : angle 1.77550 / 0.93 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 142 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7436 (mtt90) REVERT: A 126 ARG cc_start: 0.8074 (ttt-90) cc_final: 0.7853 (ttt-90) REVERT: A 173 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.5950 (tmm160) REVERT: A 232 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7257 (tmmt) REVERT: A 268 GLU cc_start: 0.6883 (mp0) cc_final: 0.6612 (mp0) REVERT: A 269 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6464 (ttm170) REVERT: A 286 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6691 (tm-30) REVERT: A 292 THR cc_start: 0.5469 (p) cc_final: 0.4870 (t) REVERT: B 11 THR cc_start: 0.4710 (OUTLIER) cc_final: 0.3403 (m) REVERT: B 255 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7711 (tpt90) REVERT: B 497 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6867 (mmtt) outliers start: 54 outliers final: 34 residues processed: 181 average time/residue: 0.4018 time to fit residues: 77.3887 Evaluate side-chains 182 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 78 GLN A 87 ASN A 193 GLN B 70 HIS B 331 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.233307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.213683 restraints weight = 5892.153| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 1.08 r_work: 0.4210 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.4133 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7046 Z= 0.163 Angle : 0.628 11.561 9528 Z= 0.333 Chirality : 0.044 0.156 1003 Planarity : 0.005 0.051 1184 Dihedral : 7.833 64.232 1005 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.81 % Favored : 94.07 % Rotamer: Outliers : 7.55 % Allowed : 22.10 % Favored : 70.35 % 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: -0.28 (0.29), residues: 826 helix: 2.03 (0.27), residues: 354 sheet: -0.52 (0.44), residues: 133 loop : -2.62 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.021 0.002 TYR A 274 PHE 0.023 0.002 PHE B 401 TRP 0.022 0.002 TRP B 336 HIS 0.008 0.001 HIS B 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 7030) covalent geometry : angle 0.62483 / 0.33 ( 9497) SS BOND : bond 0.00335 / 0.20 ( 14) SS BOND : angle 1.08563 / 0.64 ( 28) hydrogen bonds : bond 0.06711 / 4.32 ( 351) hydrogen bonds : angle 4.68786 / 3.38 ( 981) Misc. bond : bond 0.00032 / 0.02 ( 1) link_BETA1-4 : bond 0.00002 / 0.00 ( 1) link_BETA1-4 : angle 1.94506 / 1.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7339 (mtt90) REVERT: A 126 ARG cc_start: 0.8025 (ttt-90) cc_final: 0.7805 (ttt-90) REVERT: A 173 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.5878 (tmm160) REVERT: A 232 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7231 (tmmt) REVERT: A 268 GLU cc_start: 0.6834 (mp0) cc_final: 0.6581 (mp0) REVERT: A 269 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6455 (ttm170) REVERT: A 286 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6689 (tm-30) REVERT: A 292 THR cc_start: 0.5385 (p) cc_final: 0.4794 (t) REVERT: B 11 THR cc_start: 0.4990 (OUTLIER) cc_final: 0.3642 (m) REVERT: B 267 GLU cc_start: 0.6968 (pt0) cc_final: 0.6735 (pp20) REVERT: B 497 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6838 (mmtt) outliers start: 54 outliers final: 39 residues processed: 188 average time/residue: 0.4226 time to fit residues: 84.4250 Evaluate side-chains 186 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 0.0030 chunk 77 optimal weight: 1.9990 chunk 28 optimal weight: 0.0020 chunk 34 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 78 GLN A 87 ASN A 193 GLN B 70 HIS B 108 GLN B 331 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.236747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.217607 restraints weight = 5962.606| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 1.09 r_work: 0.4261 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.4165 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7046 Z= 0.128 Angle : 0.596 11.941 9528 Z= 0.311 Chirality : 0.043 0.148 1003 Planarity : 0.005 0.048 1184 Dihedral : 7.474 58.914 1005 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.96 % Favored : 94.92 % Rotamer: Outliers : 6.99 % Allowed : 22.38 % Favored : 70.63 % 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: 0.07 (0.30), residues: 826 helix: 2.35 (0.27), residues: 353 sheet: -0.44 (0.44), residues: 136 loop : -2.42 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 185 TYR 0.018 0.001 TYR A 274 PHE 0.013 0.001 PHE B 486 TRP 0.019 0.001 TRP B 336 HIS 0.007 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 7030) covalent geometry : angle 0.59406 / 0.31 ( 9497) SS BOND : bond 0.00295 / 0.17 ( 14) SS BOND : angle 0.98190 / 0.58 ( 28) hydrogen bonds : bond 0.05753 / 3.73 ( 351) hydrogen bonds : angle 4.46191 / 3.21 ( 981) Misc. bond : bond 0.00014 / 0.01 ( 1) link_BETA1-4 : bond 0.00113 / 0.06 ( 1) link_BETA1-4 : angle 1.67944 / 0.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7393 (mtt90) REVERT: A 126 ARG cc_start: 0.8103 (ttt-90) cc_final: 0.7884 (ttt-90) REVERT: A 173 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.5902 (tmm160) REVERT: A 268 GLU cc_start: 0.6683 (mp0) cc_final: 0.6423 (mp0) REVERT: A 269 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6431 (ttm170) REVERT: A 286 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6660 (tm-30) REVERT: B 11 THR cc_start: 0.4319 (OUTLIER) cc_final: 0.3084 (m) REVERT: B 267 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6609 (pp20) outliers start: 50 outliers final: 32 residues processed: 188 average time/residue: 0.4054 time to fit residues: 81.1872 Evaluate side-chains 186 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 58 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 9 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 11 optimal weight: 0.0000 chunk 21 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 78 GLN A 87 ASN A 193 GLN B 70 HIS B 331 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.236375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.217198 restraints weight = 5969.820| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 1.07 r_work: 0.4261 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.4175 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7046 Z= 0.135 Angle : 0.605 12.377 9528 Z= 0.316 Chirality : 0.043 0.148 1003 Planarity : 0.005 0.049 1184 Dihedral : 7.392 58.203 1005 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.21 % Favored : 94.67 % Rotamer: Outliers : 6.43 % Allowed : 23.08 % Favored : 70.49 % 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: 0.04 (0.30), residues: 826 helix: 2.22 (0.27), residues: 354 sheet: -0.31 (0.47), residues: 128 loop : -2.35 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 254 TYR 0.019 0.002 TYR A 274 PHE 0.018 0.001 PHE B 486 TRP 0.019 0.001 TRP B 336 HIS 0.006 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 7030) covalent geometry : angle 0.60229 / 0.32 ( 9497) SS BOND : bond 0.00311 / 0.18 ( 14) SS BOND : angle 0.99944 / 0.60 ( 28) hydrogen bonds : bond 0.05940 / 3.86 ( 351) hydrogen bonds : angle 4.52530 / 3.24 ( 981) Misc. bond : bond 0.00032 / 0.02 ( 1) link_BETA1-4 : bond 0.00040 / 0.02 ( 1) link_BETA1-4 : angle 1.74485 / 0.92 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7373 (mtt90) REVERT: A 126 ARG cc_start: 0.8031 (ttt-90) cc_final: 0.7816 (ttt-90) REVERT: A 173 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.5906 (tmm160) REVERT: A 268 GLU cc_start: 0.6625 (mp0) cc_final: 0.6367 (mm-30) REVERT: A 269 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6397 (ttm170) REVERT: A 286 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6651 (tm-30) REVERT: B 11 THR cc_start: 0.4491 (OUTLIER) cc_final: 0.3202 (m) REVERT: B 171 GLU cc_start: 0.6525 (pm20) cc_final: 0.6118 (pm20) outliers start: 46 outliers final: 33 residues processed: 180 average time/residue: 0.4347 time to fit residues: 82.6921 Evaluate side-chains 182 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 465 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 0.0770 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.0000 chunk 70 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 78 GLN A 87 ASN A 193 GLN B 70 HIS B 108 GLN B 331 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.238097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.219490 restraints weight = 5968.039| |-----------------------------------------------------------------------------| r_work (start): 0.4406 rms_B_bonded: 1.05 r_work: 0.4271 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.4174 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7046 Z= 0.129 Angle : 0.594 12.332 9528 Z= 0.311 Chirality : 0.043 0.148 1003 Planarity : 0.005 0.047 1184 Dihedral : 7.258 58.036 1005 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.72 % Favored : 95.16 % Rotamer: Outliers : 5.87 % Allowed : 24.06 % Favored : 70.07 % 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: 0.05 (0.30), residues: 826 helix: 2.30 (0.27), residues: 353 sheet: -0.43 (0.45), residues: 134 loop : -2.38 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 255 TYR 0.017 0.002 TYR A 274 PHE 0.014 0.001 PHE B 486 TRP 0.018 0.001 TRP B 336 HIS 0.014 0.001 HIS B 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 7030) covalent geometry : angle 0.59193 / 0.31 ( 9497) SS BOND : bond 0.00319 / 0.18 ( 14) SS BOND : angle 0.98658 / 0.59 ( 28) hydrogen bonds : bond 0.05652 / 3.68 ( 351) hydrogen bonds : angle 4.47200 / 3.20 ( 981) Misc. bond : bond 0.00014 / 0.01 ( 1) link_BETA1-4 : bond 0.00071 / 0.04 ( 1) link_BETA1-4 : angle 1.79325 / 0.95 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3500.75 seconds wall clock time: 60 minutes 1.97 seconds (3601.97 seconds total)