Starting phenix.real_space_refine on Sat May 10 23:06:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqf_62503/05_2025/9kqf_62503.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqf_62503/05_2025/9kqf_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_62503/05_2025/9kqf_62503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqf_62503/05_2025/9kqf_62503.map" model { file = "/net/cci-nas-00/data/ceres_data/9kqf_62503/05_2025/9kqf_62503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqf_62503/05_2025/9kqf_62503.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.72, per 1000 atoms: 0.67 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: 2.30 Conformation dependent library (CDL) restraints added in 777.1 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: 0.54 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: 1.65 Time building geometry restraints manager: 2.52 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 - 35.66: 3986 35.66 - 71.33: 260 71.33 - 106.99: 49 106.99 - 142.66: 14 142.66 - 178.32: 17 Dihedral angle restraints: 4326 sinusoidal: 2108 harmonic: 2218 Sorted by residual: dihedral pdb=" C7 T7X B 501 " pdb=" O13 T7X B 501 " pdb=" P1 T7X B 501 " pdb=" O11 T7X B 501 " ideal model delta sinusoidal sigma weight residual -41.94 136.38 -178.32 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C7 T7X B 501 " pdb=" O13 T7X B 501 " pdb=" P1 T7X B 501 " pdb=" O12 T7X B 501 " ideal model delta sinusoidal sigma weight residual 91.36 -92.00 -176.64 1 3.00e+01 1.11e-03 2.13e+01 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 ... (remaining 4323 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.910 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 26.742 178.320 2890 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.072 0.003 TRP B 387 HIS 0.004 0.001 HIS A 317 PHE 0.022 0.002 PHE A 79 TYR 0.020 0.001 TYR A 274 ARG 0.005 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.20224 ( 414) hydrogen bonds : angle 7.28278 ( 1218) covalent geometry : bond 0.00485 ( 7276) covalent geometry : angle 0.61864 ( 9782) Misc. bond : bond 0.00071 ( 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 : 0.727 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8411 (t0) cc_final: 0.7857 (t0) outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.2057 time to fit residues: 28.7697 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 : 0.731 ------------------------------------------------------------------------------- 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 62 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.0570 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3836 r_free = 0.3836 target = 0.166125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128951 restraints weight = 7611.688| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.88 r_work: 0.3100 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7283 Z= 0.134 Angle : 0.574 7.815 9782 Z= 0.282 Chirality : 0.040 0.248 1002 Planarity : 0.004 0.030 1126 Dihedral : 25.034 174.467 1483 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.98 % Allowed : 19.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.31), residues: 746 helix: 1.81 (0.22), residues: 536 sheet: None (None), residues: 0 loop : 0.22 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 387 HIS 0.002 0.001 HIS B 309 PHE 0.020 0.001 PHE A 79 TYR 0.008 0.001 TYR A 274 ARG 0.004 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 414) hydrogen bonds : angle 4.44335 ( 1218) covalent geometry : bond 0.00307 ( 7276) covalent geometry : angle 0.57419 ( 9782) Misc. bond : bond 0.00039 ( 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 136 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8611 (t0) cc_final: 0.8137 (t0) REVERT: A 134 ASP cc_start: 0.8217 (t0) cc_final: 0.7930 (t0) REVERT: A 184 ARG cc_start: 0.8708 (tpt170) cc_final: 0.8246 (tpp-160) REVERT: A 276 ARG cc_start: 0.7871 (mmt180) cc_final: 0.7641 (mmt180) REVERT: A 399 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.6893 (mp) REVERT: B 31 ASP cc_start: 0.8764 (t0) cc_final: 0.8485 (t0) REVERT: B 134 ASP cc_start: 0.8109 (t0) cc_final: 0.7748 (t0) REVERT: B 184 ARG cc_start: 0.8798 (tpt-90) cc_final: 0.8197 (ttt90) outliers start: 27 outliers final: 17 residues processed: 124 average time/residue: 0.1965 time to fit residues: 32.5073 Evaluate side-chains 115 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 265 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 47 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3738 r_free = 0.3738 target = 0.158216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119387 restraints weight = 7771.983| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.94 r_work: 0.3078 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7283 Z= 0.135 Angle : 0.537 6.989 9782 Z= 0.266 Chirality : 0.040 0.217 1002 Planarity : 0.003 0.026 1126 Dihedral : 22.997 171.449 1480 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.13 % Allowed : 19.91 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.31), residues: 746 helix: 2.16 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.22 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 387 HIS 0.003 0.001 HIS A 20 PHE 0.016 0.001 PHE A 79 TYR 0.009 0.001 TYR A 245 ARG 0.005 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 414) hydrogen bonds : angle 4.19581 ( 1218) covalent geometry : bond 0.00318 ( 7276) covalent geometry : angle 0.53701 ( 9782) Misc. bond : bond 0.00032 ( 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 127 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7236 (OUTLIER) cc_final: 0.4807 (m-10) REVERT: A 31 ASP cc_start: 0.8522 (t0) cc_final: 0.7957 (t0) REVERT: A 134 ASP cc_start: 0.8119 (t0) cc_final: 0.7717 (t0) REVERT: A 184 ARG cc_start: 0.8706 (tpt170) cc_final: 0.8274 (tpp-160) REVERT: A 242 MET cc_start: 0.8149 (mtt) cc_final: 0.7932 (mtp) REVERT: A 276 ARG cc_start: 0.7772 (mmt180) cc_final: 0.7505 (mmt180) REVERT: A 399 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.6872 (mp) REVERT: B 31 ASP cc_start: 0.8677 (t0) cc_final: 0.8305 (t0) REVERT: B 134 ASP cc_start: 0.8029 (t0) cc_final: 0.7605 (t0) REVERT: B 184 ARG cc_start: 0.8772 (tpt-90) cc_final: 0.8308 (ttt90) REVERT: B 278 PHE cc_start: 0.8589 (m-80) cc_final: 0.7964 (m-80) outliers start: 28 outliers final: 19 residues processed: 115 average time/residue: 0.1932 time to fit residues: 29.7057 Evaluate side-chains 120 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 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 381 ILE 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 41 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.158167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.119497 restraints weight = 7843.391| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.96 r_work: 0.3107 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7283 Z= 0.130 Angle : 0.548 13.965 9782 Z= 0.262 Chirality : 0.039 0.199 1002 Planarity : 0.003 0.025 1126 Dihedral : 22.521 170.114 1480 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.72 % Allowed : 19.76 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.31), residues: 746 helix: 2.29 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.17 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 387 HIS 0.007 0.001 HIS A 309 PHE 0.018 0.001 PHE B 173 TYR 0.009 0.001 TYR A 245 ARG 0.003 0.000 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 414) hydrogen bonds : angle 4.08810 ( 1218) covalent geometry : bond 0.00306 ( 7276) covalent geometry : angle 0.54760 ( 9782) Misc. bond : bond 0.00030 ( 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 134 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7226 (OUTLIER) cc_final: 0.4790 (m-10) REVERT: A 31 ASP cc_start: 0.8560 (t0) cc_final: 0.7969 (t0) REVERT: A 134 ASP cc_start: 0.8101 (t0) cc_final: 0.7750 (t0) REVERT: A 184 ARG cc_start: 0.8686 (tpt170) cc_final: 0.8288 (tpp-160) REVERT: A 242 MET cc_start: 0.8098 (mtt) cc_final: 0.7864 (mtp) REVERT: A 276 ARG cc_start: 0.7792 (mmt180) cc_final: 0.7464 (mpt180) REVERT: A 308 LYS cc_start: 0.7062 (tttp) cc_final: 0.6824 (ttpp) REVERT: A 399 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.6901 (mp) REVERT: B 17 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.5035 (m-10) REVERT: B 31 ASP cc_start: 0.8616 (t0) cc_final: 0.8198 (t0) REVERT: B 134 ASP cc_start: 0.8027 (t0) cc_final: 0.7600 (t0) REVERT: B 184 ARG cc_start: 0.8708 (tpt-90) cc_final: 0.8246 (ttt90) REVERT: B 215 TRP cc_start: 0.6732 (p-90) cc_final: 0.6039 (p-90) REVERT: B 266 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7028 (tp40) REVERT: B 278 PHE cc_start: 0.8577 (m-80) cc_final: 0.7938 (m-80) outliers start: 32 outliers final: 25 residues processed: 120 average time/residue: 0.2158 time to fit residues: 34.1137 Evaluate side-chains 128 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 64 VAL 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 266 GLN Chi-restraints excluded: chain B residue 298 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.0040 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3860 r_free = 0.3860 target = 0.168375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131605 restraints weight = 7587.864| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.87 r_work: 0.3125 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1846 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= 0.121 Angle : 0.531 12.757 9782 Z= 0.255 Chirality : 0.039 0.188 1002 Planarity : 0.003 0.028 1126 Dihedral : 21.863 167.144 1480 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.31 % Allowed : 19.62 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.31), residues: 746 helix: 2.39 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.24 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 387 HIS 0.003 0.001 HIS A 20 PHE 0.018 0.001 PHE A 79 TYR 0.009 0.001 TYR A 245 ARG 0.008 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 414) hydrogen bonds : angle 4.02869 ( 1218) covalent geometry : bond 0.00284 ( 7276) covalent geometry : angle 0.53089 ( 9782) Misc. bond : bond 0.00042 ( 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 133 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.4869 (m-10) REVERT: A 31 ASP cc_start: 0.8565 (t0) cc_final: 0.7948 (t0) REVERT: A 134 ASP cc_start: 0.8162 (t0) cc_final: 0.7798 (t0) REVERT: A 184 ARG cc_start: 0.8743 (tpt170) cc_final: 0.8363 (tpp-160) REVERT: A 242 MET cc_start: 0.8028 (mtt) cc_final: 0.7794 (mtp) REVERT: A 266 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6860 (tt0) REVERT: A 276 ARG cc_start: 0.7745 (mmt180) cc_final: 0.7415 (mpt180) REVERT: A 399 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.6922 (mp) REVERT: B 17 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.5108 (m-10) REVERT: B 31 ASP cc_start: 0.8614 (t0) cc_final: 0.8158 (t0) REVERT: B 134 ASP cc_start: 0.8062 (t0) cc_final: 0.7674 (t0) REVERT: B 184 ARG cc_start: 0.8801 (tpt-90) cc_final: 0.8586 (tpt-90) REVERT: B 266 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7037 (tp40) REVERT: B 278 PHE cc_start: 0.8509 (m-80) cc_final: 0.7969 (m-80) REVERT: B 399 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6826 (mp) outliers start: 36 outliers final: 25 residues processed: 118 average time/residue: 0.2023 time to fit residues: 31.7705 Evaluate side-chains 127 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 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 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 64 VAL Chi-restraints excluded: chain B residue 83 ILE 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 266 GLN 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 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 33 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3793 r_free = 0.3793 target = 0.161885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.124679 restraints weight = 7735.173| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.88 r_work: 0.3110 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1856 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= 0.147 Angle : 0.543 12.285 9782 Z= 0.263 Chirality : 0.040 0.199 1002 Planarity : 0.003 0.025 1126 Dihedral : 21.753 166.451 1480 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 5.90 % Allowed : 19.32 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.31), residues: 746 helix: 2.34 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.25 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 387 HIS 0.003 0.001 HIS A 309 PHE 0.019 0.001 PHE A 79 TYR 0.009 0.001 TYR A 245 ARG 0.004 0.000 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 414) hydrogen bonds : angle 4.06079 ( 1218) covalent geometry : bond 0.00355 ( 7276) covalent geometry : angle 0.54278 ( 9782) Misc. bond : bond 0.00044 ( 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 141 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.4831 (m-10) REVERT: A 31 ASP cc_start: 0.8572 (t0) cc_final: 0.7955 (t0) REVERT: A 134 ASP cc_start: 0.8114 (t0) cc_final: 0.7732 (t0) REVERT: A 184 ARG cc_start: 0.8704 (tpt170) cc_final: 0.8295 (tpp-160) REVERT: A 242 MET cc_start: 0.8018 (mtt) cc_final: 0.7788 (mtp) REVERT: A 266 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.6653 (tt0) REVERT: A 276 ARG cc_start: 0.7748 (mmt180) cc_final: 0.7386 (mpt180) REVERT: A 399 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6862 (mp) REVERT: B 17 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.5094 (m-10) REVERT: B 31 ASP cc_start: 0.8668 (t0) cc_final: 0.8188 (t0) REVERT: B 134 ASP cc_start: 0.8040 (t0) cc_final: 0.7685 (t0) REVERT: B 215 TRP cc_start: 0.6768 (p-90) cc_final: 0.5997 (p-90) REVERT: B 238 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.5889 (mpt180) REVERT: B 266 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.6911 (tp40) REVERT: B 399 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6852 (mp) outliers start: 40 outliers final: 31 residues processed: 124 average time/residue: 0.2044 time to fit residues: 33.8212 Evaluate side-chains 139 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 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 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 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 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 266 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 5 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 0.0770 chunk 36 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3855 r_free = 0.3855 target = 0.166852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.128969 restraints weight = 7511.494| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.97 r_work: 0.3131 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2044 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= 0.109 Angle : 0.517 11.907 9782 Z= 0.249 Chirality : 0.039 0.188 1002 Planarity : 0.003 0.024 1126 Dihedral : 21.142 165.163 1480 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.05 % Allowed : 19.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.31), residues: 746 helix: 2.47 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.31 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 387 HIS 0.003 0.000 HIS A 20 PHE 0.017 0.001 PHE A 79 TYR 0.008 0.001 TYR A 245 ARG 0.003 0.000 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 414) hydrogen bonds : angle 3.96398 ( 1218) covalent geometry : bond 0.00248 ( 7276) covalent geometry : angle 0.51718 ( 9782) Misc. bond : bond 0.00040 ( 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 142 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.4814 (m-10) REVERT: A 31 ASP cc_start: 0.8573 (t0) cc_final: 0.7952 (t0) REVERT: A 134 ASP cc_start: 0.8078 (t0) cc_final: 0.7719 (t0) REVERT: A 182 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7703 (mm) REVERT: A 184 ARG cc_start: 0.8700 (tpt170) cc_final: 0.8385 (tpp-160) REVERT: A 276 ARG cc_start: 0.7752 (mmt180) cc_final: 0.7476 (mpt180) REVERT: A 308 LYS cc_start: 0.7090 (tttp) cc_final: 0.6816 (ttpp) REVERT: A 399 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.6895 (mp) REVERT: B 17 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.4995 (m-10) REVERT: B 31 ASP cc_start: 0.8665 (t0) cc_final: 0.8153 (t0) REVERT: B 134 ASP cc_start: 0.8032 (t0) cc_final: 0.7666 (t0) REVERT: B 184 ARG cc_start: 0.8670 (tpt-90) cc_final: 0.8047 (ttt90) REVERT: B 215 TRP cc_start: 0.6694 (p-90) cc_final: 0.5930 (p-90) REVERT: B 238 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.6165 (tpp80) REVERT: B 266 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.6931 (tp40) REVERT: B 278 PHE cc_start: 0.8429 (m-80) cc_final: 0.7907 (m-80) REVERT: B 399 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6786 (mp) outliers start: 41 outliers final: 30 residues processed: 128 average time/residue: 0.1948 time to fit residues: 32.9616 Evaluate side-chains 136 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 36 PHE 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 167 ILE 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 275 VAL 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 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 130 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 266 GLN 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 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 44 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 54 optimal weight: 0.0040 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 55 optimal weight: 6.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.166092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128517 restraints weight = 7532.085| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.98 r_work: 0.3201 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7283 Z= 0.099 Angle : 0.520 14.195 9782 Z= 0.247 Chirality : 0.038 0.179 1002 Planarity : 0.003 0.024 1126 Dihedral : 20.407 163.564 1480 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.90 % Allowed : 19.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.31), residues: 746 helix: 2.55 (0.22), residues: 540 sheet: None (None), residues: 0 loop : 0.44 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 387 HIS 0.003 0.000 HIS A 20 PHE 0.015 0.001 PHE A 79 TYR 0.007 0.001 TYR A 245 ARG 0.004 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 414) hydrogen bonds : angle 3.90780 ( 1218) covalent geometry : bond 0.00217 ( 7276) covalent geometry : angle 0.51986 ( 9782) Misc. bond : bond 0.00032 ( 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 144 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.4838 (m-10) REVERT: A 31 ASP cc_start: 0.8607 (t0) cc_final: 0.7990 (t0) REVERT: A 134 ASP cc_start: 0.8085 (t0) cc_final: 0.7709 (t0) REVERT: A 182 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7693 (mm) REVERT: A 184 ARG cc_start: 0.8651 (tpt170) cc_final: 0.8322 (tpp-160) REVERT: A 308 LYS cc_start: 0.7111 (tttp) cc_final: 0.6856 (ttpp) REVERT: A 399 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.6858 (mp) REVERT: B 31 ASP cc_start: 0.8671 (t0) cc_final: 0.8164 (t0) REVERT: B 134 ASP cc_start: 0.8104 (t0) cc_final: 0.7741 (t0) REVERT: B 215 TRP cc_start: 0.6646 (p-90) cc_final: 0.5861 (p-90) REVERT: B 242 MET cc_start: 0.8624 (mtt) cc_final: 0.8335 (mtp) REVERT: B 266 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7144 (tp40) REVERT: B 278 PHE cc_start: 0.8393 (m-80) cc_final: 0.7875 (m-80) REVERT: B 399 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6807 (mp) outliers start: 40 outliers final: 31 residues processed: 133 average time/residue: 0.2015 time to fit residues: 35.5524 Evaluate side-chains 138 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 275 VAL 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 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 266 GLN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 31 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3885 r_free = 0.3885 target = 0.169396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.131146 restraints weight = 7619.332| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.02 r_work: 0.3138 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7283 Z= 0.115 Angle : 0.530 13.341 9782 Z= 0.254 Chirality : 0.039 0.190 1002 Planarity : 0.003 0.025 1126 Dihedral : 20.306 161.543 1480 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.95 % Favored : 96.92 % Rotamer: Outliers : 5.31 % Allowed : 20.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.31), residues: 746 helix: 2.57 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.40 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 387 HIS 0.003 0.000 HIS A 20 PHE 0.020 0.001 PHE A 313 TYR 0.007 0.001 TYR A 274 ARG 0.004 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 414) hydrogen bonds : angle 3.92095 ( 1218) covalent geometry : bond 0.00266 ( 7276) covalent geometry : angle 0.52951 ( 9782) Misc. bond : bond 0.00031 ( 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 136 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7279 (OUTLIER) cc_final: 0.4758 (m-10) REVERT: A 31 ASP cc_start: 0.8542 (t0) cc_final: 0.7877 (t0) REVERT: A 134 ASP cc_start: 0.8051 (t0) cc_final: 0.7681 (t0) REVERT: A 182 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7649 (mm) REVERT: A 184 ARG cc_start: 0.8603 (tpt170) cc_final: 0.8264 (tpp-160) REVERT: A 266 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6954 (tt0) REVERT: A 276 ARG cc_start: 0.7842 (mpt180) cc_final: 0.7526 (mmt180) REVERT: A 278 PHE cc_start: 0.8369 (m-80) cc_final: 0.7950 (m-80) REVERT: A 308 LYS cc_start: 0.7066 (tttp) cc_final: 0.6787 (ttpp) REVERT: A 399 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6633 (mp) REVERT: B 31 ASP cc_start: 0.8677 (t0) cc_final: 0.8152 (t0) REVERT: B 134 ASP cc_start: 0.8012 (t0) cc_final: 0.7667 (t0) REVERT: B 184 ARG cc_start: 0.8776 (tpt-90) cc_final: 0.8064 (ttt90) REVERT: B 217 GLN cc_start: 0.7224 (mm110) cc_final: 0.6587 (mm110) REVERT: B 238 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.6218 (tpp80) REVERT: B 266 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.6955 (tp40) REVERT: B 278 PHE cc_start: 0.8384 (m-80) cc_final: 0.7868 (m-80) REVERT: B 399 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6757 (mp) outliers start: 36 outliers final: 29 residues processed: 125 average time/residue: 0.2004 time to fit residues: 33.0750 Evaluate side-chains 135 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 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 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 266 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 45 optimal weight: 0.6980 chunk 57 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 0.0570 chunk 23 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.161960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.122498 restraints weight = 7781.502| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.09 r_work: 0.3129 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7283 Z= 0.113 Angle : 0.528 13.174 9782 Z= 0.253 Chirality : 0.039 0.193 1002 Planarity : 0.003 0.026 1126 Dihedral : 20.056 158.713 1480 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.82 % Favored : 97.05 % Rotamer: Outliers : 5.16 % Allowed : 20.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.31), residues: 746 helix: 2.58 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.41 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 387 HIS 0.003 0.000 HIS A 20 PHE 0.016 0.001 PHE A 313 TYR 0.006 0.001 TYR A 245 ARG 0.003 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 414) hydrogen bonds : angle 3.91556 ( 1218) covalent geometry : bond 0.00258 ( 7276) covalent geometry : angle 0.52821 ( 9782) Misc. bond : bond 0.00032 ( 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 136 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.4846 (m-10) REVERT: A 31 ASP cc_start: 0.8593 (t0) cc_final: 0.7939 (t0) REVERT: A 134 ASP cc_start: 0.8081 (t0) cc_final: 0.7711 (t0) REVERT: A 182 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7682 (mm) REVERT: A 184 ARG cc_start: 0.8530 (tpt170) cc_final: 0.8172 (tpp-160) REVERT: A 266 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6816 (tt0) REVERT: A 276 ARG cc_start: 0.7738 (mpt180) cc_final: 0.7357 (mmt180) REVERT: A 278 PHE cc_start: 0.8262 (m-80) cc_final: 0.7847 (m-80) REVERT: A 308 LYS cc_start: 0.7006 (tttp) cc_final: 0.6761 (ttpp) REVERT: A 399 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6631 (mp) REVERT: B 31 ASP cc_start: 0.8656 (t0) cc_final: 0.8140 (t0) REVERT: B 134 ASP cc_start: 0.8014 (t0) cc_final: 0.7697 (t0) REVERT: B 184 ARG cc_start: 0.8677 (tpt-90) cc_final: 0.8307 (tpt-90) REVERT: B 266 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.6857 (tp40) REVERT: B 278 PHE cc_start: 0.8271 (m-80) cc_final: 0.7744 (m-80) REVERT: B 399 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6750 (mp) outliers start: 35 outliers final: 28 residues processed: 125 average time/residue: 0.1918 time to fit residues: 32.0420 Evaluate side-chains 136 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 298 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 52 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 17 optimal weight: 0.0060 chunk 25 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.163553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124507 restraints weight = 7638.364| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.06 r_work: 0.3157 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7283 Z= 0.100 Angle : 0.513 12.882 9782 Z= 0.246 Chirality : 0.038 0.184 1002 Planarity : 0.003 0.026 1126 Dihedral : 19.607 157.164 1480 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.55 % Favored : 97.32 % Rotamer: Outliers : 5.46 % Allowed : 19.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.31), residues: 746 helix: 2.62 (0.22), residues: 540 sheet: None (None), residues: 0 loop : 0.47 (0.47), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 387 HIS 0.002 0.000 HIS A 20 PHE 0.016 0.001 PHE A 313 TYR 0.006 0.001 TYR A 339 ARG 0.003 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 414) hydrogen bonds : angle 3.86692 ( 1218) covalent geometry : bond 0.00219 ( 7276) covalent geometry : angle 0.51255 ( 9782) Misc. bond : bond 0.00025 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3357.05 seconds wall clock time: 59 minutes 5.15 seconds (3545.15 seconds total)