Starting phenix.real_space_refine on Wed Aug 5 08:58:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hnv_34919/08_2026/8hnv_34919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnv_34919/08_2026/8hnv_34919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8hnv_34919/08_2026/8hnv_34919.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hnv_34919/08_2026/8hnv_34919.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hnv_34919/08_2026/8hnv_34919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnv_34919/08_2026/8hnv_34919.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hnv_34919/08_2026/8hnv_34919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnv_34919/08_2026/8hnv_34919.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 127 5.49 5 S 20 5.16 5 C 5381 2.51 5 N 1623 2.21 5 O 2045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9196 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5821 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 25, 'TRANS': 719} Chain breaks: 9 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 2, 'TYR:plan': 4, 'GLU:plan': 8, 'PHE:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 128 Chain: "B" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2046 Classifications: {'RNAv2': 97} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 45, 'rna3p_pyr': 46} Link IDs: {'rna2p': 5, 'rna3p': 91} Chain breaks: 3 Chain: "C" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "E" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 692 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Time building chain proxies: 1.64, per 1000 atoms: 0.18 Number of scatterers: 9196 At special positions: 0 Unit cell: (119.6, 106.08, 108.16, 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 20 16.00 P 127 15.00 O 2045 8.00 N 1623 7.00 C 5381 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=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 151.3 milliseconds 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 8 sheets defined 51.3% alpha, 10.6% beta 48 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 54 through 86 removed outlier: 4.032A pdb=" N SER A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 109 removed outlier: 3.693A pdb=" N LEU A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 127 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.949A pdb=" N GLU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 removed outlier: 3.944A pdb=" N HIS A 191 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.572A pdb=" N LYS A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 295 removed outlier: 3.986A pdb=" N LEU A 294 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.597A pdb=" N LYS A 301 " --> pdb=" O GLN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.638A pdb=" N GLN A 308 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 309 " --> pdb=" O TYR A 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 305 through 309' Processing helix chain 'A' and resid 343 through 356 removed outlier: 3.989A pdb=" N ASN A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 368 removed outlier: 3.768A pdb=" N TRP A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.985A pdb=" N LEU A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 417 through 430 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 467 through 489 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 692 through 703 removed outlier: 3.947A pdb=" N THR A 696 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 715 through 722 removed outlier: 4.089A pdb=" N ASP A 719 " --> pdb=" O HIS A 715 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 720 " --> pdb=" O HIS A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 771 through 779 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 829 through 832 removed outlier: 3.574A pdb=" N GLU A 832 " --> pdb=" O ARG A 829 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 829 through 832' Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 845 through 851 Processing helix chain 'A' and resid 858 through 872 removed outlier: 4.136A pdb=" N TYR A 862 " --> pdb=" O GLU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 880 Processing helix chain 'A' and resid 938 through 944 Processing helix chain 'A' and resid 956 through 960 removed outlier: 3.989A pdb=" N TRP A 960 " --> pdb=" O GLU A 957 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 12 removed outlier: 3.667A pdb=" N ILE E 11 " --> pdb=" O ASN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 20 Processing helix chain 'E' and resid 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 24 through 44 Proline residue: E 30 - end of helix removed outlier: 3.523A pdb=" N SER E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 50 Processing helix chain 'E' and resid 55 through 84 removed outlier: 4.188A pdb=" N ALA E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 removed outlier: 3.744A pdb=" N ALA A 13 " --> pdb=" O GLY A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 9 removed outlier: 3.894A pdb=" N ASP A 37 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLU A 25 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU A 35 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 494 through 496 removed outlier: 6.697A pdb=" N ILE A 494 " --> pdb=" O PHE A 689 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AA5, first strand: chain 'A' and resid 834 through 840 Processing sheet with id=AA6, first strand: chain 'A' and resid 884 through 885 removed outlier: 4.392A pdb=" N PHE A 884 " --> pdb=" O VAL A 892 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 930 through 937 removed outlier: 3.750A pdb=" N PHE A 971 " --> pdb=" O VAL A 924 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR A 926 " --> pdb=" O PHE A 969 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE A 969 " --> pdb=" O THR A 926 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1018 through 1022 removed outlier: 3.623A pdb=" N ILE A1004 " --> pdb=" O PHE A1019 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A1021 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE A1002 " --> pdb=" O GLY A1021 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 978 " --> pdb=" O TYR A1033 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A1029 " --> pdb=" O VAL A 982 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN A1034 " --> pdb=" O ARG A1043 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A1043 " --> pdb=" O GLN A1034 " (cutoff:3.500A) 285 hydrogen bonds defined for protein. 825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 113 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2297 1.34 - 1.45: 2342 1.45 - 1.57: 4690 1.57 - 1.69: 249 1.69 - 1.81: 35 Bond restraints: 9613 Sorted by residual: bond pdb=" C3' DC C 7 " pdb=" C2' DC C 7 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DT C 13 " pdb=" C2' DT C 13 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.18e+00 bond pdb=" C1' DT D 31 " pdb=" N1 DT D 31 " ideal model delta sigma weight residual 1.468 1.500 -0.032 1.40e-02 5.10e+03 5.12e+00 bond pdb=" C3' DT C 18 " pdb=" C2' DT C 18 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.60e+00 bond pdb=" C3' DG C 12 " pdb=" C2' DG C 12 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.60e+00 ... (remaining 9608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 12857 1.44 - 2.89: 560 2.89 - 4.33: 104 4.33 - 5.77: 23 5.77 - 7.22: 6 Bond angle restraints: 13550 Sorted by residual: angle pdb=" C3' U B 76 " pdb=" O3' U B 76 " pdb=" P U B 77 " ideal model delta sigma weight residual 119.70 126.20 -6.50 1.20e+00 6.94e-01 2.93e+01 angle pdb=" N3 DT D 32 " pdb=" C4 DT D 32 " pdb=" O4 DT D 32 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT D 31 " pdb=" C4 DT D 31 " pdb=" O4 DT D 31 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT D 26 " pdb=" C4 DT D 26 " pdb=" O4 DT D 26 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT D 28 " pdb=" C4 DT D 28 " pdb=" O4 DT D 28 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 13545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.61: 5176 34.61 - 69.23: 357 69.23 - 103.84: 10 103.84 - 138.45: 0 138.45 - 173.06: 6 Dihedral angle restraints: 5549 sinusoidal: 3134 harmonic: 2415 Sorted by residual: dihedral pdb=" C4' C B 83 " pdb=" C3' C B 83 " pdb=" C2' C B 83 " pdb=" C1' C B 83 " ideal model delta sinusoidal sigma weight residual 36.34 -35.40 71.74 1 3.10e+00 1.04e-01 6.86e+02 dihedral pdb=" C4' U B 125 " pdb=" C3' U B 125 " pdb=" C2' U B 125 " pdb=" C1' U B 125 " ideal model delta sinusoidal sigma weight residual 36.35 -34.53 70.88 1 3.10e+00 1.04e-01 6.72e+02 dihedral pdb=" C4' C B 88 " pdb=" C3' C B 88 " pdb=" C2' C B 88 " pdb=" C1' C B 88 " ideal model delta sinusoidal sigma weight residual 36.35 -34.51 70.85 1 3.10e+00 1.04e-01 6.71e+02 ... (remaining 5546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1417 0.073 - 0.147: 95 0.147 - 0.220: 17 0.220 - 0.294: 92 0.294 - 0.367: 3 Chirality restraints: 1624 Sorted by residual: chirality pdb=" P U B 77 " pdb=" OP1 U B 77 " pdb=" OP2 U B 77 " pdb=" O5' U B 77 " both_signs ideal model delta sigma weight residual True 2.17 -2.54 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" P U B 93 " pdb=" OP1 U B 93 " pdb=" OP2 U B 93 " pdb=" O5' U B 93 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" P C B 95 " pdb=" OP1 C B 95 " pdb=" OP2 C B 95 " pdb=" O5' C B 95 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 1621 not shown) Planarity restraints: 1264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 253 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C GLU A 253 " 0.040 2.00e-02 2.50e+03 pdb=" O GLU A 253 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR A 254 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 166 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO A 167 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 974 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.92e+00 pdb=" N PRO A 975 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.024 5.00e-02 4.00e+02 ... (remaining 1261 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 216 2.66 - 3.22: 8279 3.22 - 3.78: 15958 3.78 - 4.34: 21788 4.34 - 4.90: 32021 Nonbonded interactions: 78262 Sorted by model distance: nonbonded pdb=" O ILE A 891 " pdb=" O2' U B 56 " model vdw 2.103 3.040 nonbonded pdb=" O HIS A 98 " pdb=" O2' U B 59 " model vdw 2.134 3.040 nonbonded pdb=" O2' G B 69 " pdb=" O ASN E 26 " model vdw 2.158 3.040 nonbonded pdb=" OP1 U B 124 " pdb=" NZ LYS E 32 " model vdw 2.159 3.120 nonbonded pdb=" O2' G B 92 " pdb=" OP1 U B 93 " model vdw 2.162 3.040 ... (remaining 78257 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.480 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9613 Z= 0.218 Angle : 0.713 7.216 13550 Z= 0.401 Chirality : 0.072 0.367 1624 Planarity : 0.004 0.054 1264 Dihedral : 19.430 173.064 3973 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.30), residues: 810 helix: 0.77 (0.29), residues: 339 sheet: -0.99 (0.63), residues: 72 loop : -0.93 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 114 TYR 0.012 0.001 TYR A 164 PHE 0.017 0.001 PHE A 266 TRP 0.018 0.001 TRP A 117 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.22 ( 9613) covalent geometry : angle 0.71317 / 0.40 (13550) hydrogen bonds : bond 0.15737 / 10.59 ( 396) hydrogen bonds : angle 6.43192 / 4.62 ( 1039) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.192 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0910 time to fit residues: 13.4818 Evaluate side-chains 82 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN A 348 GLN A 482 ASN A 976 ASN A1034 GLN E 51 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.188331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159317 restraints weight = 11064.679| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.28 r_work: 0.3624 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9613 Z= 0.267 Angle : 1.002 16.370 13550 Z= 0.428 Chirality : 0.082 1.363 1624 Planarity : 0.005 0.045 1264 Dihedral : 19.259 175.074 2379 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.18 % Allowed : 11.76 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.29), residues: 810 helix: 0.51 (0.28), residues: 362 sheet: -0.93 (0.68), residues: 63 loop : -1.32 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 128 TYR 0.010 0.002 TYR A 254 PHE 0.016 0.002 PHE E 8 TRP 0.031 0.002 TRP A 231 HIS 0.005 0.001 HIS A 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.27 ( 9613) covalent geometry : angle 1.00177 / 0.43 (13550) hydrogen bonds : bond 0.05784 / 4.00 ( 396) hydrogen bonds : angle 5.02277 / 3.66 ( 1039) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 873 ASN cc_start: 0.5797 (t0) cc_final: 0.5540 (p0) outliers start: 8 outliers final: 6 residues processed: 88 average time/residue: 0.0757 time to fit residues: 9.7113 Evaluate side-chains 80 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain E residue 6 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 91 optimal weight: 4.9990 chunk 63 optimal weight: 0.0870 chunk 19 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 GLN A 901 GLN E 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.187969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157605 restraints weight = 11001.723| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.33 r_work: 0.3605 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9613 Z= 0.204 Angle : 0.838 15.313 13550 Z= 0.370 Chirality : 0.069 1.087 1624 Planarity : 0.004 0.051 1264 Dihedral : 19.245 178.962 2379 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.76 % Allowed : 13.82 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.29), residues: 810 helix: 0.62 (0.28), residues: 366 sheet: -0.84 (0.67), residues: 65 loop : -1.40 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 195 TYR 0.010 0.002 TYR A 254 PHE 0.017 0.002 PHE A 216 TRP 0.008 0.002 TRP A 117 HIS 0.003 0.001 HIS A 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 ( 9613) covalent geometry : angle 0.83781 / 0.37 (13550) hydrogen bonds : bond 0.05187 / 3.47 ( 396) hydrogen bonds : angle 4.76079 / 3.47 ( 1039) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.160 Fit side-chains REVERT: A 189 TYR cc_start: 0.7784 (m-80) cc_final: 0.7543 (m-80) REVERT: A 919 MET cc_start: 0.7613 (mtt) cc_final: 0.7401 (mtm) outliers start: 12 outliers final: 8 residues processed: 85 average time/residue: 0.0652 time to fit residues: 8.3587 Evaluate side-chains 79 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain E residue 6 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 GLN E 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.188759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159639 restraints weight = 11136.473| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.31 r_work: 0.3622 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9613 Z= 0.171 Angle : 0.783 16.394 13550 Z= 0.349 Chirality : 0.064 1.076 1624 Planarity : 0.004 0.054 1264 Dihedral : 19.286 178.577 2379 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.47 % Allowed : 16.32 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.29), residues: 810 helix: 0.75 (0.28), residues: 364 sheet: -0.84 (0.68), residues: 65 loop : -1.35 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 829 TYR 0.011 0.001 TYR A 254 PHE 0.017 0.002 PHE A 216 TRP 0.028 0.002 TRP A 231 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 9613) covalent geometry : angle 0.78304 / 0.35 (13550) hydrogen bonds : bond 0.04655 / 3.16 ( 396) hydrogen bonds : angle 4.56899 / 3.36 ( 1039) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.227 Fit side-chains REVERT: A 1034 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6565 (tp40) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 0.0590 time to fit residues: 7.6386 Evaluate side-chains 77 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain E residue 6 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 13 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 GLN A 873 ASN A 976 ASN E 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.185027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.163935 restraints weight = 11109.796| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 0.92 r_work: 0.3659 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 9613 Z= 0.342 Angle : 1.000 15.198 13550 Z= 0.441 Chirality : 0.072 0.819 1624 Planarity : 0.006 0.058 1264 Dihedral : 19.417 179.045 2379 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.09 % Allowed : 17.65 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.28), residues: 810 helix: 0.11 (0.27), residues: 366 sheet: -1.17 (0.65), residues: 65 loop : -1.58 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 478 TYR 0.017 0.003 TYR A 254 PHE 0.023 0.003 PHE A 216 TRP 0.037 0.003 TRP A 231 HIS 0.006 0.002 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.34 ( 9613) covalent geometry : angle 1.00039 / 0.44 (13550) hydrogen bonds : bond 0.06441 / 4.42 ( 396) hydrogen bonds : angle 4.93443 / 3.62 ( 1039) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.181 Fit side-chains REVERT: A 35 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7888 (pp) REVERT: A 358 LEU cc_start: 0.6776 (mt) cc_final: 0.6464 (mp) outliers start: 21 outliers final: 17 residues processed: 91 average time/residue: 0.0694 time to fit residues: 9.3765 Evaluate side-chains 85 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 6 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 GLN A 803 GLN A1001 ASN E 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.188174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.166449 restraints weight = 11162.404| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 0.90 r_work: 0.3694 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9613 Z= 0.193 Angle : 0.830 14.922 13550 Z= 0.370 Chirality : 0.063 0.817 1624 Planarity : 0.004 0.059 1264 Dihedral : 19.353 176.607 2379 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.24 % Allowed : 16.91 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.29), residues: 810 helix: 0.44 (0.27), residues: 369 sheet: -1.08 (0.66), residues: 65 loop : -1.41 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 71 TYR 0.013 0.002 TYR A 254 PHE 0.020 0.002 PHE A 216 TRP 0.040 0.002 TRP A 231 HIS 0.004 0.001 HIS A 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 ( 9613) covalent geometry : angle 0.82964 / 0.37 (13550) hydrogen bonds : bond 0.05062 / 3.46 ( 396) hydrogen bonds : angle 4.67486 / 3.43 ( 1039) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.181 Fit side-chains REVERT: A 35 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7784 (pp) REVERT: A 230 MET cc_start: 0.7742 (mmm) cc_final: 0.7515 (tpt) REVERT: A 358 LEU cc_start: 0.6746 (mt) cc_final: 0.6445 (mp) outliers start: 22 outliers final: 16 residues processed: 90 average time/residue: 0.0677 time to fit residues: 8.8686 Evaluate side-chains 87 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 10 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 GLN E 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.190515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.168613 restraints weight = 11050.975| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 0.91 r_work: 0.3697 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9613 Z= 0.155 Angle : 0.774 14.069 13550 Z= 0.345 Chirality : 0.060 0.787 1624 Planarity : 0.004 0.057 1264 Dihedral : 19.303 178.712 2379 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.65 % Allowed : 17.65 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.29), residues: 810 helix: 0.68 (0.28), residues: 372 sheet: -1.07 (0.64), residues: 73 loop : -1.37 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1043 TYR 0.014 0.001 TYR A 254 PHE 0.021 0.001 PHE A 216 TRP 0.041 0.002 TRP A 231 HIS 0.003 0.001 HIS A 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 9613) covalent geometry : angle 0.77428 / 0.34 (13550) hydrogen bonds : bond 0.04531 / 3.09 ( 396) hydrogen bonds : angle 4.46357 / 3.28 ( 1039) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.205 Fit side-chains REVERT: A 114 ARG cc_start: 0.7175 (ttm110) cc_final: 0.6808 (ttp-170) REVERT: A 179 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6320 (mm-30) REVERT: A 949 LYS cc_start: 0.7629 (mmtp) cc_final: 0.7413 (mmmt) outliers start: 18 outliers final: 13 residues processed: 88 average time/residue: 0.0827 time to fit residues: 10.5042 Evaluate side-chains 84 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 10 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 17 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1001 ASN E 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.189578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.172454 restraints weight = 10987.762| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 0.70 r_work: 0.3753 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9613 Z= 0.178 Angle : 0.792 13.164 13550 Z= 0.352 Chirality : 0.061 0.743 1624 Planarity : 0.004 0.058 1264 Dihedral : 19.260 179.581 2379 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.79 % Allowed : 18.68 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.29), residues: 810 helix: 0.68 (0.28), residues: 372 sheet: -1.01 (0.66), residues: 65 loop : -1.43 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 478 TYR 0.016 0.002 TYR A 164 PHE 0.025 0.002 PHE A 669 TRP 0.044 0.002 TRP A 231 HIS 0.003 0.001 HIS A 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 ( 9613) covalent geometry : angle 0.79203 / 0.35 (13550) hydrogen bonds : bond 0.04727 / 3.23 ( 396) hydrogen bonds : angle 4.42674 / 3.23 ( 1039) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.172 Fit side-chains REVERT: A 35 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7808 (pp) REVERT: A 179 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6431 (mm-30) REVERT: A 358 LEU cc_start: 0.6683 (mt) cc_final: 0.6354 (mp) REVERT: A 949 LYS cc_start: 0.7777 (mmtp) cc_final: 0.7529 (mmmt) outliers start: 19 outliers final: 15 residues processed: 89 average time/residue: 0.0712 time to fit residues: 9.2393 Evaluate side-chains 87 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 10 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.7980 chunk 62 optimal weight: 0.0050 chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 90 optimal weight: 0.2980 chunk 70 optimal weight: 10.0000 chunk 73 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN E 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.194724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.173711 restraints weight = 11050.616| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 0.90 r_work: 0.3776 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9613 Z= 0.125 Angle : 0.734 13.250 13550 Z= 0.327 Chirality : 0.058 0.780 1624 Planarity : 0.004 0.057 1264 Dihedral : 19.246 179.356 2379 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.06 % Allowed : 19.56 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.29), residues: 810 helix: 0.86 (0.28), residues: 372 sheet: -0.89 (0.65), residues: 72 loop : -1.32 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 472 TYR 0.018 0.001 TYR A 254 PHE 0.016 0.001 PHE A 216 TRP 0.031 0.002 TRP A 231 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 9613) covalent geometry : angle 0.73363 / 0.33 (13550) hydrogen bonds : bond 0.04027 / 2.71 ( 396) hydrogen bonds : angle 4.21233 / 3.07 ( 1039) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.233 Fit side-chains REVERT: A 114 ARG cc_start: 0.7198 (ttm110) cc_final: 0.6755 (ttp-170) REVERT: A 179 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6520 (mm-30) REVERT: A 949 LYS cc_start: 0.7615 (mmtp) cc_final: 0.7408 (mmmt) outliers start: 14 outliers final: 11 residues processed: 85 average time/residue: 0.0709 time to fit residues: 9.0677 Evaluate side-chains 81 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 977 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 58 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN E 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.191726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.174113 restraints weight = 11027.658| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 0.75 r_work: 0.3772 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9613 Z= 0.171 Angle : 0.770 12.474 13550 Z= 0.343 Chirality : 0.059 0.725 1624 Planarity : 0.004 0.058 1264 Dihedral : 19.174 178.101 2379 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.50 % Allowed : 19.26 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.29), residues: 810 helix: 0.86 (0.28), residues: 369 sheet: -0.91 (0.67), residues: 65 loop : -1.36 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 478 TYR 0.014 0.002 TYR A 254 PHE 0.019 0.002 PHE A 216 TRP 0.045 0.003 TRP A 231 HIS 0.004 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 ( 9613) covalent geometry : angle 0.77023 / 0.34 (13550) hydrogen bonds : bond 0.04390 / 2.99 ( 396) hydrogen bonds : angle 4.28607 / 3.12 ( 1039) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.173 Fit side-chains REVERT: A 179 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6466 (mm-30) REVERT: A 358 LEU cc_start: 0.6705 (mt) cc_final: 0.6416 (mp) REVERT: A 949 LYS cc_start: 0.7724 (mmtp) cc_final: 0.7494 (mmmt) outliers start: 17 outliers final: 13 residues processed: 85 average time/residue: 0.0679 time to fit residues: 8.6114 Evaluate side-chains 83 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain E residue 86 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 9 optimal weight: 0.0980 chunk 88 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.191999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.175791 restraints weight = 10936.020| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 0.70 r_work: 0.3799 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 9613 Z= 0.182 Angle : 1.009 58.902 13550 Z= 0.529 Chirality : 0.059 0.724 1624 Planarity : 0.004 0.058 1264 Dihedral : 19.172 178.201 2379 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.35 % Allowed : 18.97 % Favored : 78.68 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.29), residues: 810 helix: 0.85 (0.28), residues: 368 sheet: -0.90 (0.67), residues: 65 loop : -1.35 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 478 TYR 0.015 0.001 TYR A 254 PHE 0.016 0.001 PHE A 216 TRP 0.040 0.002 TRP A 231 HIS 0.003 0.001 HIS A 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 9613) covalent geometry : angle 1.00879 / 0.53 (13550) hydrogen bonds : bond 0.04349 / 2.96 ( 396) hydrogen bonds : angle 4.28166 / 3.12 ( 1039) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1686.60 seconds wall clock time: 29 minutes 31.58 seconds (1771.58 seconds total)