Starting phenix.real_space_refine on Thu Jul 2 05:53:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqf_62503/07_2026/9kqf_62503.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqf_62503/07_2026/9kqf_62503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kqf_62503/07_2026/9kqf_62503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqf_62503/07_2026/9kqf_62503.map" model { file = "/net/cci-nas-00/data/ceres_data/9kqf_62503/07_2026/9kqf_62503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqf_62503/07_2026/9kqf_62503.cif" } resolution = 3.25 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= 0.002 sd= 0.061 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 16 5.49 5 S 40 5.16 5 C 4830 2.51 5 N 1016 2.21 5 O 1164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s 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: 7066 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3171 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 364} Chain breaks: 1 Chain: "B" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3171 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 364} Chain breaks: 1 Chain: "A" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 400 Unusual residues: {'C14': 1, 'D12': 1, 'LBN': 6, 'PSF': 2, 'T7X': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'LBN:plan-3': 3} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 324 Unusual residues: {'C14': 1, 'D12': 1, 'LBN': 4, 'PSF': 2, 'T7X': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 1.48, per 1000 atoms: 0.21 Number of scatterers: 7066 At special positions: 0 Unit cell: (91.785, 108.665, 71.74, 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 40 16.00 P 16 15.00 O 1164 8.00 N 1016 7.00 C 4830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 354.5 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1436 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 77.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 14 through 26 removed outlier: 3.566A pdb=" N ILE A 24 " --> pdb=" O HIS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 38 Processing helix chain 'A' and resid 41 through 59 Processing helix chain 'A' and resid 64 through 88 Processing helix chain 'A' and resid 97 through 119 removed outlier: 3.915A pdb=" N TRP A 101 " --> pdb=" O HIS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 135 through 138 Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.618A pdb=" N HIS A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 165' Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 185 through 203 removed outlier: 4.289A pdb=" N THR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 224 through 243 Processing helix chain 'A' and resid 255 through 267 removed outlier: 4.302A pdb=" N PHE A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 312 Processing helix chain 'A' and resid 317 through 344 removed outlier: 4.159A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 351 through 372 Processing helix chain 'A' and resid 381 through 408 removed outlier: 4.173A pdb=" N LEU A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 26 removed outlier: 3.632A pdb=" N ILE B 24 " --> pdb=" O HIS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 38 Processing helix chain 'B' and resid 43 through 59 removed outlier: 3.501A pdb=" N THR B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 88 removed outlier: 3.691A pdb=" N ILE B 69 " --> pdb=" O PRO B 65 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 119 removed outlier: 3.923A pdb=" N TRP B 101 " --> pdb=" O HIS B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 134 Processing helix chain 'B' and resid 135 through 138 Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.603A pdb=" N HIS B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 160 through 165' Processing helix chain 'B' and resid 166 through 184 removed outlier: 3.651A pdb=" N LEU B 182 " --> pdb=" O MET B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 203 removed outlier: 4.329A pdb=" N THR B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 224 through 242 removed outlier: 3.685A pdb=" N MET B 242 " --> pdb=" O ARG B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 267 removed outlier: 4.251A pdb=" N PHE B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 311 removed outlier: 3.560A pdb=" N LYS B 308 " --> pdb=" O THR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 344 removed outlier: 4.246A pdb=" N ARG B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 3.650A pdb=" N ARG B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 372 removed outlier: 3.949A pdb=" N ALA B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 408 removed outlier: 4.230A pdb=" N LEU B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 399 " --> pdb=" O THR B 395 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1028 1.32 - 1.44: 2201 1.44 - 1.57: 3953 1.57 - 1.69: 32 1.69 - 1.81: 62 Bond restraints: 7276 Sorted by residual: bond pdb=" CG1 ILE B 192 " pdb=" CD1 ILE B 192 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.37e+00 bond pdb=" CA ALA A 332 " pdb=" C ALA A 332 " ideal model delta sigma weight residual 1.521 1.533 -0.012 1.11e-02 8.12e+03 1.08e+00 bond pdb=" CG1 ILE B 330 " pdb=" CD1 ILE B 330 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.08e+00 bond pdb=" CG LEU A 53 " pdb=" CD2 LEU A 53 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" C GLY A 328 " pdb=" O GLY A 328 " ideal model delta sigma weight residual 1.234 1.246 -0.012 1.19e-02 7.06e+03 9.48e-01 ... (remaining 7271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 9621 1.98 - 3.97: 129 3.97 - 5.95: 22 5.95 - 7.93: 8 7.93 - 9.92: 2 Bond angle restraints: 9782 Sorted by residual: angle pdb=" N ILE A 381 " pdb=" CA ILE A 381 " pdb=" C ILE A 381 " ideal model delta sigma weight residual 113.07 105.96 7.11 1.36e+00 5.41e-01 2.73e+01 angle pdb=" C LEU B 386 " pdb=" N TRP B 387 " pdb=" CA TRP B 387 " ideal model delta sigma weight residual 121.58 111.66 9.92 1.95e+00 2.63e-01 2.59e+01 angle pdb=" C LEU A 386 " pdb=" N TRP A 387 " pdb=" CA TRP A 387 " ideal model delta sigma weight residual 121.14 113.01 8.13 1.75e+00 3.27e-01 2.16e+01 angle pdb=" N ILE B 381 " pdb=" CA ILE B 381 " pdb=" C ILE B 381 " ideal model delta sigma weight residual 112.98 107.20 5.78 1.25e+00 6.40e-01 2.14e+01 angle pdb=" N TRP B 387 " pdb=" CA TRP B 387 " pdb=" CB TRP B 387 " ideal model delta sigma weight residual 110.41 117.34 -6.93 1.68e+00 3.54e-01 1.70e+01 ... (remaining 9777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 3941 35.13 - 70.26: 260 70.26 - 105.39: 27 105.39 - 140.53: 11 140.53 - 175.66: 13 Dihedral angle restraints: 4252 sinusoidal: 2034 harmonic: 2218 Sorted by residual: dihedral pdb=" N1 LBN A 511 " pdb=" C6 LBN A 511 " pdb=" C9 LBN A 511 " pdb=" O2 LBN A 511 " ideal model delta sinusoidal sigma weight residual 71.48 -104.18 175.66 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N1 LBN A 508 " pdb=" C6 LBN A 508 " pdb=" C9 LBN A 508 " pdb=" O2 LBN A 508 " ideal model delta sinusoidal sigma weight residual 71.48 -101.60 173.08 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN A 503 " pdb=" C2 LBN A 503 " pdb=" C3 LBN A 503 " pdb=" O7 LBN A 503 " ideal model delta sinusoidal sigma weight residual 62.67 -96.44 159.11 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 4249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 737 0.045 - 0.090: 225 0.090 - 0.135: 34 0.135 - 0.181: 4 0.181 - 0.226: 2 Chirality restraints: 1002 Sorted by residual: chirality pdb=" C1 T7X B 501 " pdb=" C2 T7X B 501 " pdb=" C6 T7X B 501 " pdb=" O1 T7X B 501 " both_signs ideal model delta sigma weight residual False -2.42 -2.19 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C1 T7X A 510 " pdb=" C2 T7X A 510 " pdb=" C6 T7X A 510 " pdb=" O1 T7X A 510 " both_signs ideal model delta sigma weight residual False -2.42 -2.23 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA ILE A 381 " pdb=" N ILE A 381 " pdb=" C ILE A 381 " pdb=" CB ILE A 381 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 999 not shown) Planarity restraints: 1126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 387 " 0.023 2.00e-02 2.50e+03 2.82e-02 1.98e+01 pdb=" CG TRP B 387 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP B 387 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP B 387 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 387 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 387 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 387 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 387 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 387 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP B 387 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 387 " -0.024 2.00e-02 2.50e+03 2.76e-02 1.91e+01 pdb=" CG TRP A 387 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP A 387 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP A 387 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 387 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 387 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 387 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 387 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 387 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 387 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 184 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C ARG B 184 " 0.032 2.00e-02 2.50e+03 pdb=" O ARG B 184 " -0.013 2.00e-02 2.50e+03 pdb=" N SER B 185 " -0.011 2.00e-02 2.50e+03 ... (remaining 1123 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 282 2.72 - 3.27: 7096 3.27 - 3.81: 11696 3.81 - 4.36: 14283 4.36 - 4.90: 24352 Nonbonded interactions: 57709 Sorted by model distance: nonbonded pdb=" O LEU B 265 " pdb=" OG1 THR B 268 " model vdw 2.176 3.040 nonbonded pdb=" OH TYR A 291 " pdb=" O LEU A 388 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR B 291 " pdb=" O LEU B 388 " model vdw 2.230 3.040 nonbonded pdb=" OE1 GLU B 200 " pdb=" NE2 GLN B 217 " model vdw 2.240 3.120 nonbonded pdb=" O TYR B 55 " pdb=" OG1 THR B 59 " model vdw 2.263 3.040 ... (remaining 57704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 408 or resid 502 or resid 504 or resid 508 thro \ ugh 509)) selection = (chain 'B' and (resid 14 through 408 or resid 502 or (resid 504 and (name C1 or \ name C12 or name C15 or name C18 or name C2 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C3 or name C30 or name C34 or name C35 or name C \ 36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C6 or nam \ e C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 or name O \ 6 or name O7 or name O8 or name P1 )) or (resid 508 and (name C1 or name C10 or \ name C12 or name C13 or name C15 or name C16 or name C18 or name C19 or name C2 \ or name C21 or name C25 or name C26 or name C27 or name C28 or name C29 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or na \ me C36 or name C37 or name C4 or name C6 or name C7 or name C9 or name N1 or nam \ e O1 or name O2 or name O3 or name O4 or name O5 or name O6 or name O7 or name O \ 8 or name P1 )) or resid 509)) } 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: 1.190 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.460 Find NCS groups from input model: 0.090 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.005 0.046 7283 Z= 0.200 Angle : 0.619 9.915 9782 Z= 0.323 Chirality : 0.042 0.226 1002 Planarity : 0.004 0.035 1126 Dihedral : 24.687 175.657 2816 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.29 % Allowed : 22.27 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.73 (0.31), residues: 746 helix: 0.74 (0.22), residues: 530 sheet: None (None), residues: 0 loop : 0.14 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 276 TYR 0.020 0.001 TYR A 274 PHE 0.022 0.002 PHE A 79 TRP 0.072 0.003 TRP B 387 HIS 0.004 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 ( 7276) covalent geometry : angle 0.61862 / 0.32 ( 9782) hydrogen bonds : bond 0.20224 / 13.17 ( 414) hydrogen bonds : angle 7.28278 / 5.29 ( 1218) Misc. bond : bond 0.00071 / 0.04 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8410 (t0) cc_final: 0.7857 (t0) outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.0795 time to fit residues: 11.2382 Evaluate side-chains 102 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 GLN A 309 HIS ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.158255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120164 restraints weight = 7859.294| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.94 r_work: 0.3082 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7283 Z= 0.128 Angle : 0.568 7.971 9782 Z= 0.280 Chirality : 0.041 0.274 1002 Planarity : 0.004 0.029 1126 Dihedral : 24.215 174.606 1409 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.54 % Allowed : 20.06 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.31), residues: 746 helix: 1.81 (0.22), residues: 536 sheet: None (None), residues: 0 loop : 0.23 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 276 TYR 0.008 0.001 TYR A 186 PHE 0.019 0.001 PHE A 79 TRP 0.058 0.002 TRP B 387 HIS 0.002 0.001 HIS B 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 7276) covalent geometry : angle 0.56790 / 0.28 ( 9782) hydrogen bonds : bond 0.04571 / 3.08 ( 414) hydrogen bonds : angle 4.49197 / 3.26 ( 1218) Misc. bond : bond 0.00036 / 0.02 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8594 (t0) cc_final: 0.8091 (t0) REVERT: A 134 ASP cc_start: 0.8170 (t0) cc_final: 0.7886 (t0) REVERT: A 184 ARG cc_start: 0.8706 (tpt170) cc_final: 0.8177 (tmt-80) REVERT: A 242 MET cc_start: 0.8174 (mtt) cc_final: 0.7968 (mtm) REVERT: B 31 ASP cc_start: 0.8727 (t0) cc_final: 0.8417 (t0) REVERT: B 134 ASP cc_start: 0.8095 (t0) cc_final: 0.7736 (t0) REVERT: B 184 ARG cc_start: 0.8774 (tpt-90) cc_final: 0.8245 (ttt90) outliers start: 24 outliers final: 15 residues processed: 122 average time/residue: 0.0753 time to fit residues: 12.3689 Evaluate side-chains 113 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 395 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 HIS ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.156339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117448 restraints weight = 7786.508| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.95 r_work: 0.3075 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7283 Z= 0.151 Angle : 0.563 7.841 9782 Z= 0.276 Chirality : 0.041 0.269 1002 Planarity : 0.003 0.026 1126 Dihedral : 22.762 172.098 1406 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.42 % Allowed : 19.32 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.31), residues: 746 helix: 2.06 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.18 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 276 TYR 0.011 0.001 TYR A 274 PHE 0.018 0.001 PHE A 79 TRP 0.057 0.002 TRP B 387 HIS 0.003 0.001 HIS A 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 7276) covalent geometry : angle 0.56350 / 0.28 ( 9782) hydrogen bonds : bond 0.04287 / 2.90 ( 414) hydrogen bonds : angle 4.25012 / 3.09 ( 1218) Misc. bond : bond 0.00033 / 0.02 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8508 (t0) cc_final: 0.7952 (t0) REVERT: A 134 ASP cc_start: 0.8157 (t0) cc_final: 0.7755 (t0) REVERT: A 184 ARG cc_start: 0.8657 (tpt170) cc_final: 0.8235 (tpp-160) REVERT: A 242 MET cc_start: 0.8214 (mtt) cc_final: 0.7974 (mtp) REVERT: A 276 ARG cc_start: 0.7956 (mpt180) cc_final: 0.7730 (mmt180) REVERT: A 399 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.6922 (mp) REVERT: B 31 ASP cc_start: 0.8681 (t0) cc_final: 0.8308 (t0) REVERT: B 134 ASP cc_start: 0.8078 (t0) cc_final: 0.7671 (t0) REVERT: B 215 TRP cc_start: 0.6738 (p-90) cc_final: 0.6029 (p-90) outliers start: 30 outliers final: 22 residues processed: 120 average time/residue: 0.0741 time to fit residues: 11.9171 Evaluate side-chains 124 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 44 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.157609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.119329 restraints weight = 7851.937| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.93 r_work: 0.3061 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7283 Z= 0.155 Angle : 0.577 13.961 9782 Z= 0.277 Chirality : 0.041 0.271 1002 Planarity : 0.003 0.026 1126 Dihedral : 22.349 170.644 1406 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.90 % Allowed : 18.73 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.31), residues: 746 helix: 2.17 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.13 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 276 TYR 0.009 0.001 TYR A 245 PHE 0.017 0.001 PHE B 173 TRP 0.057 0.002 TRP B 387 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 7276) covalent geometry : angle 0.57716 / 0.28 ( 9782) hydrogen bonds : bond 0.04193 / 2.85 ( 414) hydrogen bonds : angle 4.18386 / 3.04 ( 1218) Misc. bond : bond 0.00036 / 0.02 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.4815 (m-10) REVERT: A 31 ASP cc_start: 0.8533 (t0) cc_final: 0.7956 (t0) REVERT: A 134 ASP cc_start: 0.8176 (t0) cc_final: 0.7798 (t0) REVERT: A 184 ARG cc_start: 0.8656 (tpt170) cc_final: 0.8318 (tpp-160) REVERT: A 242 MET cc_start: 0.8235 (mtt) cc_final: 0.7998 (mtp) REVERT: A 276 ARG cc_start: 0.7938 (mpt180) cc_final: 0.7697 (mmt180) REVERT: A 308 LYS cc_start: 0.7112 (tttp) cc_final: 0.6873 (ttpp) REVERT: A 399 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.6963 (mp) REVERT: B 17 TYR cc_start: 0.7466 (OUTLIER) cc_final: 0.5061 (m-10) REVERT: B 31 ASP cc_start: 0.8639 (t0) cc_final: 0.8225 (t0) REVERT: B 134 ASP cc_start: 0.8053 (t0) cc_final: 0.7629 (t0) REVERT: B 215 TRP cc_start: 0.6796 (p-90) cc_final: 0.6028 (p-90) outliers start: 40 outliers final: 30 residues processed: 124 average time/residue: 0.0835 time to fit residues: 13.7525 Evaluate side-chains 132 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 402 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 64 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 HIS A 309 HIS ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.166402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.129224 restraints weight = 7675.522| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.90 r_work: 0.3115 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7283 Z= 0.123 Angle : 0.540 12.600 9782 Z= 0.260 Chirality : 0.040 0.261 1002 Planarity : 0.003 0.024 1126 Dihedral : 21.491 168.444 1406 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.01 % Allowed : 19.62 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.31), residues: 746 helix: 2.32 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.19 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 276 TYR 0.010 0.001 TYR A 245 PHE 0.019 0.001 PHE A 79 TRP 0.055 0.002 TRP B 387 HIS 0.002 0.001 HIS A 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 7276) covalent geometry : angle 0.53951 / 0.26 ( 9782) hydrogen bonds : bond 0.03843 / 2.62 ( 414) hydrogen bonds : angle 4.06862 / 2.96 ( 1218) Misc. bond : bond 0.00032 / 0.02 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7261 (OUTLIER) cc_final: 0.4827 (m-10) REVERT: A 31 ASP cc_start: 0.8555 (t0) cc_final: 0.7944 (t0) REVERT: A 134 ASP cc_start: 0.8127 (t0) cc_final: 0.7747 (t0) REVERT: A 184 ARG cc_start: 0.8689 (tpt170) cc_final: 0.8354 (tpp-160) REVERT: A 242 MET cc_start: 0.8139 (mtt) cc_final: 0.7880 (mtp) REVERT: A 266 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6746 (tt0) REVERT: A 276 ARG cc_start: 0.7883 (mpt180) cc_final: 0.7601 (mmt180) REVERT: A 399 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.6943 (mp) REVERT: B 17 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.5076 (m-10) REVERT: B 31 ASP cc_start: 0.8611 (t0) cc_final: 0.8160 (t0) REVERT: B 134 ASP cc_start: 0.8045 (t0) cc_final: 0.7647 (t0) REVERT: B 184 ARG cc_start: 0.8692 (tpt-90) cc_final: 0.8082 (ttt90) REVERT: B 215 TRP cc_start: 0.6763 (p-90) cc_final: 0.6016 (p-90) REVERT: B 246 HIS cc_start: 0.7047 (t70) cc_final: 0.6847 (t70) REVERT: B 276 ARG cc_start: 0.8328 (mmm-85) cc_final: 0.7993 (mmm160) outliers start: 34 outliers final: 26 residues processed: 123 average time/residue: 0.0712 time to fit residues: 11.7073 Evaluate side-chains 130 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.0270 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 HIS ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.160853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123268 restraints weight = 7788.682| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.92 r_work: 0.3112 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7283 Z= 0.116 Angle : 0.536 12.357 9782 Z= 0.258 Chirality : 0.040 0.255 1002 Planarity : 0.003 0.024 1126 Dihedral : 21.222 167.845 1406 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.46 % Allowed : 19.62 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.31), residues: 746 helix: 2.35 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.24 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 276 TYR 0.008 0.001 TYR A 245 PHE 0.018 0.001 PHE A 79 TRP 0.054 0.002 TRP B 387 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 7276) covalent geometry : angle 0.53567 / 0.26 ( 9782) hydrogen bonds : bond 0.03780 / 2.58 ( 414) hydrogen bonds : angle 4.03632 / 2.94 ( 1218) Misc. bond : bond 0.00030 / 0.01 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.4810 (m-10) REVERT: A 31 ASP cc_start: 0.8550 (t0) cc_final: 0.7915 (t0) REVERT: A 134 ASP cc_start: 0.8098 (t0) cc_final: 0.7715 (t0) REVERT: A 182 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7704 (mm) REVERT: A 184 ARG cc_start: 0.8647 (tpt170) cc_final: 0.8311 (tpp-160) REVERT: A 242 MET cc_start: 0.8114 (mtt) cc_final: 0.7859 (mtp) REVERT: A 266 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6774 (tt0) REVERT: A 276 ARG cc_start: 0.7938 (mpt180) cc_final: 0.7640 (mmt180) REVERT: A 399 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6854 (mp) REVERT: B 17 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.5111 (m-10) REVERT: B 31 ASP cc_start: 0.8604 (t0) cc_final: 0.8120 (t0) REVERT: B 134 ASP cc_start: 0.8010 (t0) cc_final: 0.7574 (t0) REVERT: B 215 TRP cc_start: 0.6749 (p-90) cc_final: 0.5991 (p-90) outliers start: 37 outliers final: 30 residues processed: 124 average time/residue: 0.0737 time to fit residues: 12.5006 Evaluate side-chains 134 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 58 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.158544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.120942 restraints weight = 7727.475| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.90 r_work: 0.3074 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7283 Z= 0.158 Angle : 0.565 12.054 9782 Z= 0.273 Chirality : 0.041 0.267 1002 Planarity : 0.003 0.026 1126 Dihedral : 21.288 165.232 1406 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 6.64 % Allowed : 18.88 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.31), residues: 746 helix: 2.29 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.25 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 276 TYR 0.009 0.001 TYR A 245 PHE 0.020 0.001 PHE A 79 TRP 0.055 0.002 TRP B 387 HIS 0.003 0.001 HIS A 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 7276) covalent geometry : angle 0.56547 / 0.27 ( 9782) hydrogen bonds : bond 0.04115 / 2.81 ( 414) hydrogen bonds : angle 4.08151 / 2.97 ( 1218) Misc. bond : bond 0.00038 / 0.02 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 99 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.4805 (m-10) REVERT: A 31 ASP cc_start: 0.8585 (t0) cc_final: 0.7942 (t0) REVERT: A 134 ASP cc_start: 0.8146 (t0) cc_final: 0.7750 (t0) REVERT: A 182 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7813 (mm) REVERT: A 184 ARG cc_start: 0.8642 (tpt170) cc_final: 0.8283 (tpp-160) REVERT: A 242 MET cc_start: 0.8113 (mtt) cc_final: 0.7848 (mtp) REVERT: A 266 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6501 (tt0) REVERT: A 276 ARG cc_start: 0.7961 (mpt180) cc_final: 0.7705 (mmt180) REVERT: A 399 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6812 (mp) REVERT: B 17 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.5115 (m-10) REVERT: B 31 ASP cc_start: 0.8697 (t0) cc_final: 0.8189 (t0) REVERT: B 134 ASP cc_start: 0.8038 (t0) cc_final: 0.7655 (t0) REVERT: B 215 TRP cc_start: 0.6773 (p-90) cc_final: 0.5971 (p-90) REVERT: B 238 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.6207 (tpp80) REVERT: B 399 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6879 (mp) outliers start: 45 outliers final: 35 residues processed: 127 average time/residue: 0.0766 time to fit residues: 13.1362 Evaluate side-chains 140 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.160960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.123483 restraints weight = 7806.769| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.92 r_work: 0.3112 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7283 Z= 0.117 Angle : 0.549 14.393 9782 Z= 0.260 Chirality : 0.040 0.246 1002 Planarity : 0.003 0.025 1126 Dihedral : 20.693 165.236 1406 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 6.49 % Allowed : 18.58 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.31), residues: 746 helix: 2.42 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.27 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 276 TYR 0.007 0.001 TYR A 245 PHE 0.017 0.001 PHE A 79 TRP 0.053 0.002 TRP B 387 HIS 0.002 0.001 HIS A 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 7276) covalent geometry : angle 0.54896 / 0.26 ( 9782) hydrogen bonds : bond 0.03757 / 2.56 ( 414) hydrogen bonds : angle 3.99884 / 2.91 ( 1218) Misc. bond : bond 0.00040 / 0.02 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7239 (OUTLIER) cc_final: 0.4805 (m-10) REVERT: A 31 ASP cc_start: 0.8549 (t0) cc_final: 0.7902 (t0) REVERT: A 134 ASP cc_start: 0.8110 (t0) cc_final: 0.7733 (t0) REVERT: A 182 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7760 (mm) REVERT: A 184 ARG cc_start: 0.8595 (tpt170) cc_final: 0.8292 (tpp-160) REVERT: A 242 MET cc_start: 0.7996 (mtt) cc_final: 0.7747 (mtp) REVERT: A 266 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6791 (tt0) REVERT: A 276 ARG cc_start: 0.7965 (mpt180) cc_final: 0.7740 (mmt180) REVERT: A 399 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6840 (mp) REVERT: B 17 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.5047 (m-10) REVERT: B 31 ASP cc_start: 0.8684 (t0) cc_final: 0.8152 (t0) REVERT: B 134 ASP cc_start: 0.8008 (t0) cc_final: 0.7639 (t0) REVERT: B 184 ARG cc_start: 0.8764 (tpt-90) cc_final: 0.8078 (ttt90) REVERT: B 215 TRP cc_start: 0.6753 (OUTLIER) cc_final: 0.5942 (p-90) REVERT: B 238 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.6320 (tpp80) REVERT: B 278 PHE cc_start: 0.8429 (m-80) cc_final: 0.7915 (m-80) outliers start: 44 outliers final: 34 residues processed: 129 average time/residue: 0.0635 time to fit residues: 10.9853 Evaluate side-chains 138 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 215 TRP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 4 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.158635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.121242 restraints weight = 7731.434| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.90 r_work: 0.3114 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7283 Z= 0.120 Angle : 0.546 13.735 9782 Z= 0.261 Chirality : 0.040 0.221 1002 Planarity : 0.003 0.026 1126 Dihedral : 20.399 163.185 1406 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 5.75 % Allowed : 19.91 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.31), residues: 746 helix: 2.46 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.32 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 276 TYR 0.008 0.001 TYR A 186 PHE 0.017 0.001 PHE A 79 TRP 0.052 0.002 TRP B 387 HIS 0.003 0.000 HIS A 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 7276) covalent geometry : angle 0.54595 / 0.26 ( 9782) hydrogen bonds : bond 0.03770 / 2.57 ( 414) hydrogen bonds : angle 3.99247 / 2.91 ( 1218) Misc. bond : bond 0.00035 / 0.02 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.4810 (m-10) REVERT: A 31 ASP cc_start: 0.8580 (t0) cc_final: 0.7929 (t0) REVERT: A 134 ASP cc_start: 0.8134 (t0) cc_final: 0.7742 (t0) REVERT: A 182 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7723 (mm) REVERT: A 184 ARG cc_start: 0.8614 (tpt170) cc_final: 0.8264 (tpp-160) REVERT: A 242 MET cc_start: 0.7954 (mtt) cc_final: 0.7728 (mtp) REVERT: A 266 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6720 (tt0) REVERT: A 276 ARG cc_start: 0.8007 (mpt180) cc_final: 0.7700 (mmt180) REVERT: A 336 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7902 (mmt-90) REVERT: A 399 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6835 (mp) REVERT: B 31 ASP cc_start: 0.8685 (t0) cc_final: 0.8179 (t0) REVERT: B 134 ASP cc_start: 0.8019 (t0) cc_final: 0.7701 (t0) REVERT: B 184 ARG cc_start: 0.8765 (tpt-90) cc_final: 0.8104 (ttt90) REVERT: B 217 GLN cc_start: 0.7317 (mm110) cc_final: 0.6657 (mm110) REVERT: B 238 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6337 (tpp80) REVERT: B 278 PHE cc_start: 0.8435 (m-80) cc_final: 0.7916 (m-80) REVERT: B 399 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6815 (mp) outliers start: 39 outliers final: 32 residues processed: 130 average time/residue: 0.0619 time to fit residues: 10.8338 Evaluate side-chains 142 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 25 optimal weight: 0.0770 chunk 17 optimal weight: 0.0370 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.163904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124908 restraints weight = 7670.413| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.08 r_work: 0.3171 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7283 Z= 0.107 Angle : 0.533 13.406 9782 Z= 0.256 Chirality : 0.039 0.198 1002 Planarity : 0.003 0.026 1126 Dihedral : 19.882 161.398 1406 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.16 % Allowed : 20.21 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.31), residues: 746 helix: 2.56 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.37 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 276 TYR 0.006 0.001 TYR A 339 PHE 0.015 0.001 PHE A 79 TRP 0.050 0.002 TRP A 387 HIS 0.002 0.000 HIS A 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 7276) covalent geometry : angle 0.53339 / 0.26 ( 9782) hydrogen bonds : bond 0.03568 / 2.44 ( 414) hydrogen bonds : angle 3.94037 / 2.87 ( 1218) Misc. bond : bond 0.00030 / 0.01 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.4835 (m-10) REVERT: A 31 ASP cc_start: 0.8506 (t0) cc_final: 0.7858 (t0) REVERT: A 134 ASP cc_start: 0.8078 (t0) cc_final: 0.7687 (t0) REVERT: A 182 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7710 (mm) REVERT: A 184 ARG cc_start: 0.8521 (tpt170) cc_final: 0.8200 (tpp-160) REVERT: A 242 MET cc_start: 0.7864 (mtt) cc_final: 0.7598 (mtp) REVERT: A 276 ARG cc_start: 0.7921 (mpt180) cc_final: 0.7709 (mmt180) REVERT: A 308 LYS cc_start: 0.7020 (tttp) cc_final: 0.6733 (ttpp) REVERT: A 336 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7760 (mmt-90) REVERT: A 399 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6800 (mp) REVERT: B 31 ASP cc_start: 0.8645 (t0) cc_final: 0.8140 (t0) REVERT: B 134 ASP cc_start: 0.8056 (t0) cc_final: 0.7719 (t0) REVERT: B 184 ARG cc_start: 0.8679 (tpt-90) cc_final: 0.8080 (ttt90) REVERT: B 238 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6429 (tpp80) REVERT: B 278 PHE cc_start: 0.8300 (m-80) cc_final: 0.7788 (m-80) REVERT: B 399 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6766 (mp) outliers start: 35 outliers final: 28 residues processed: 129 average time/residue: 0.0754 time to fit residues: 12.9314 Evaluate side-chains 138 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 387 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 0.0670 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.161687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.122556 restraints weight = 7652.056| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.07 r_work: 0.3133 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7283 Z= 0.115 Angle : 0.538 13.132 9782 Z= 0.258 Chirality : 0.040 0.205 1002 Planarity : 0.003 0.027 1126 Dihedral : 19.735 159.637 1406 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.31 % Allowed : 20.06 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.31), residues: 746 helix: 2.58 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.34 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 276 TYR 0.007 0.001 TYR A 186 PHE 0.016 0.001 PHE A 79 TRP 0.050 0.002 TRP A 387 HIS 0.002 0.000 HIS A 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 7276) covalent geometry : angle 0.53806 / 0.26 ( 9782) hydrogen bonds : bond 0.03646 / 2.49 ( 414) hydrogen bonds : angle 3.94563 / 2.87 ( 1218) Misc. bond : bond 0.00027 / 0.01 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1450.78 seconds wall clock time: 25 minutes 33.27 seconds (1533.27 seconds total)