Starting phenix.real_space_refine on Fri Jul 3 07:26:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pp6_17796/07_2026/8pp6_17796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pp6_17796/07_2026/8pp6_17796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pp6_17796/07_2026/8pp6_17796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pp6_17796/07_2026/8pp6_17796.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pp6_17796/07_2026/8pp6_17796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pp6_17796/07_2026/8pp6_17796.map" } resolution = 3.18 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= 0.004 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 311 5.49 5 S 19 5.16 5 C 7396 2.51 5 N 2487 2.21 5 O 3104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13318 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 808 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 742 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 832 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 753 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3180 Classifications: {'DNA': 156} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 155} Chain: "J" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3214 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "K" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 283 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "M" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12495 SG CYS K 27 64.981 84.416 37.321 1.00133.28 S ATOM 12514 SG CYS K 30 63.315 85.615 34.414 1.00141.72 S ATOM 12602 SG CYS K 41 62.188 86.617 38.206 1.00135.85 S ATOM 12622 SG CYS K 44 61.221 83.403 36.536 1.00137.92 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LYS A 36 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 36 " occ=0.00 residue: pdb=" N ARG A 129 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG A 129 " occ=0.00 residue: pdb=" N LYS E 36 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS E 36 " occ=0.00 residue: pdb=" N LYS H 122 " occ=0.00 ... (8 atoms not shown) pdb=" OXT LYS H 122 " occ=0.00 Time building chain proxies: 3.12, per 1000 atoms: 0.23 Number of scatterers: 13318 At special positions: 0 Unit cell: (117.058, 124.716, 123.622, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 19 16.00 P 311 15.00 O 3104 8.00 N 2487 7.00 C 7396 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: 1.03 Conformation dependent library (CDL) restraints added in 459.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 27 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 44 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 30 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 41 " Number of angles added : 6 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1634 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 66.2% alpha, 4.6% beta 139 base pairs and 284 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.096A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.562A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.072A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.586A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 44 through 72 removed outlier: 4.547A pdb=" N VAL C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 89 removed outlier: 3.552A pdb=" N LEU C 82 " --> pdb=" O ILE C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.555A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.546A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.524A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.059A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 15 through 21 Processing helix chain 'G' and resid 25 through 35 Processing helix chain 'G' and resid 44 through 72 removed outlier: 4.346A pdb=" N VAL G 48 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL G 61 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 89 removed outlier: 3.743A pdb=" N LEU G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.866A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'M' and resid 22 through 34 removed outlier: 3.521A pdb=" N VAL M 26 " --> pdb=" O THR M 22 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE M 30 " --> pdb=" O VAL M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.867A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 41 through 42 removed outlier: 7.060A pdb=" N ARG C 41 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 99 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 41 through 42 removed outlier: 7.071A pdb=" N ARG G 41 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 76 through 77 Processing sheet with id=AA9, first strand: chain 'K' and resid 24 through 25 Processing sheet with id=AB1, first strand: chain 'M' and resid 12 through 16 removed outlier: 3.844A pdb=" N LEU M 69 " --> pdb=" O LYS M 6 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 720 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 284 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2782 1.33 - 1.46: 4521 1.46 - 1.58: 6230 1.58 - 1.70: 621 1.70 - 1.82: 32 Bond restraints: 14186 Sorted by residual: bond pdb=" C3' DT J 14 " pdb=" C2' DT J 14 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.35e+01 bond pdb=" C3' DG J -37 " pdb=" C2' DG J -37 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC J 24 " pdb=" C2' DC J 24 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC I -73 " pdb=" C2' DC I -73 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DC I 21 " pdb=" C2' DC I 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 ... (remaining 14181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 18112 1.10 - 2.20: 1839 2.20 - 3.29: 509 3.29 - 4.39: 15 4.39 - 5.49: 10 Bond angle restraints: 20485 Sorted by residual: angle pdb=" N3 DT I 71 " pdb=" C4 DT I 71 " pdb=" O4 DT I 71 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT J -50 " pdb=" C4 DT J -50 " pdb=" O4 DT J -50 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT J 22 " pdb=" C4 DT J 22 " pdb=" O4 DT J 22 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J 69 " pdb=" C4 DT J 69 " pdb=" O4 DT J 69 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT I -39 " pdb=" C4 DT I -39 " pdb=" O4 DT I -39 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 ... (remaining 20480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.13: 5751 26.13 - 52.25: 1670 52.25 - 78.38: 336 78.38 - 104.50: 1 104.50 - 130.63: 1 Dihedral angle restraints: 7759 sinusoidal: 5232 harmonic: 2527 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sinusoidal sigma weight residual 220.00 89.37 130.63 1 3.50e+01 8.16e-04 1.29e+01 dihedral pdb=" CG ARG C 70 " pdb=" CD ARG C 70 " pdb=" NE ARG C 70 " pdb=" CZ ARG C 70 " ideal model delta sinusoidal sigma weight residual 90.00 134.18 -44.18 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG F 78 " pdb=" CD ARG F 78 " pdb=" NE ARG F 78 " pdb=" CZ ARG F 78 " ideal model delta sinusoidal sigma weight residual -180.00 -136.22 -43.78 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 7756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1294 0.033 - 0.067: 654 0.067 - 0.100: 263 0.100 - 0.134: 111 0.134 - 0.167: 5 Chirality restraints: 2327 Sorted by residual: chirality pdb=" C3' DT J -67 " pdb=" C4' DT J -67 " pdb=" O3' DT J -67 " pdb=" C2' DT J -67 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" C3' DC J 7 " pdb=" C4' DC J 7 " pdb=" O3' DC J 7 " pdb=" C2' DC J 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" C3' DA I -66 " pdb=" C4' DA I -66 " pdb=" O3' DA I -66 " pdb=" C2' DA I -66 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.24e-01 ... (remaining 2324 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.025 2.00e-02 2.50e+03 1.05e-02 3.29e+00 pdb=" N9 DG I 47 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -55 " -0.021 2.00e-02 2.50e+03 9.12e-03 2.50e+00 pdb=" N9 DG I -55 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DG I -55 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I -55 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I -55 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I -55 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG I -55 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I -55 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I -55 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I -55 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I -55 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG I -55 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 36 " 0.021 2.00e-02 2.50e+03 1.03e-02 2.41e+00 pdb=" N1 DC I 36 " -0.019 2.00e-02 2.50e+03 pdb=" C2 DC I 36 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 36 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DC I 36 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 36 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 36 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 36 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC I 36 " -0.005 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2422 2.79 - 3.32: 10621 3.32 - 3.85: 24345 3.85 - 4.37: 29835 4.37 - 4.90: 41911 Nonbonded interactions: 109134 Sorted by model distance: nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.263 3.040 nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 2.360 3.040 nonbonded pdb=" OE1 GLU H 73 " pdb=" NH2 ARG H 76 " model vdw 2.398 3.120 nonbonded pdb=" O LEU E 61 " pdb=" NH1 ARG F 36 " model vdw 2.419 3.120 nonbonded pdb=" OG1 THR D 85 " pdb=" OP1 DA J -34 " model vdw 2.429 3.040 ... (remaining 109129 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' selection = (chain 'E' and resid 36 through 133) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 29 through 122) } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.770 Find NCS groups from input model: 0.130 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.006 0.039 14190 Z= 0.553 Angle : 0.734 13.065 20491 Z= 0.635 Chirality : 0.047 0.167 2327 Planarity : 0.004 0.046 1513 Dihedral : 26.622 130.630 6125 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.14 % Allowed : 11.19 % Favored : 88.68 % 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: 1.64 (0.28), residues: 852 helix: 2.20 (0.22), residues: 542 sheet: 0.73 (1.53), residues: 18 loop : -1.10 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 70 TYR 0.012 0.002 TYR B 72 PHE 0.015 0.002 PHE K 39 TRP 0.010 0.002 TRP K 25 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.55 (14186) covalent geometry : angle 0.72176 / 0.64 (20485) hydrogen bonds : bond 0.13402 / 8.89 ( 790) hydrogen bonds : angle 3.74001 / 2.75 ( 1971) metal coordination : bond 0.00683 / 0.35 ( 4) metal coordination : angle 7.86947 / 3.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 318 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 LYS cc_start: 0.7642 (tttp) cc_final: 0.7429 (tttm) REVERT: K 25 TRP cc_start: 0.8057 (p-90) cc_final: 0.7686 (p-90) outliers start: 1 outliers final: 1 residues processed: 318 average time/residue: 0.1528 time to fit residues: 64.5682 Evaluate side-chains 256 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 30.0000 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 18 ASN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.084801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.056385 restraints weight = 36592.727| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.71 r_work: 0.2747 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14190 Z= 0.157 Angle : 0.686 24.798 20491 Z= 0.382 Chirality : 0.043 0.203 2327 Planarity : 0.005 0.040 1513 Dihedral : 29.586 131.643 4377 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.27 % Allowed : 18.28 % Favored : 78.44 % 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: 1.99 (0.29), residues: 852 helix: 2.48 (0.22), residues: 548 sheet: -0.87 (1.03), residues: 28 loop : -0.90 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 33 TYR 0.026 0.003 TYR F 88 PHE 0.013 0.001 PHE K 39 TRP 0.013 0.003 TRP K 25 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.16 (14186) covalent geometry : angle 0.63835 / 0.38 (20485) hydrogen bonds : bond 0.06134 / 4.09 ( 790) hydrogen bonds : angle 3.13785 / 2.29 ( 1971) metal coordination : bond 0.01861 / 0.94 ( 4) metal coordination : angle 14.62206 / 6.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 279 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8525 (mmp80) cc_final: 0.7990 (mmm-85) REVERT: D 32 GLU cc_start: 0.8465 (pt0) cc_final: 0.8200 (pt0) REVERT: E 42 ARG cc_start: 0.8940 (mtp180) cc_final: 0.8591 (mtp85) REVERT: E 59 GLU cc_start: 0.7883 (pm20) cc_final: 0.7630 (pm20) REVERT: F 25 ASN cc_start: 0.8968 (m-40) cc_final: 0.8667 (m-40) REVERT: M 45 PHE cc_start: 0.8236 (t80) cc_final: 0.7794 (t80) outliers start: 24 outliers final: 16 residues processed: 288 average time/residue: 0.1206 time to fit residues: 47.7366 Evaluate side-chains 273 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 257 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 55 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 47 optimal weight: 0.0170 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 68 GLN G 18 ASN G 83 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.083291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.055012 restraints weight = 37020.550| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.68 r_work: 0.2722 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14190 Z= 0.175 Angle : 0.640 17.320 20491 Z= 0.364 Chirality : 0.042 0.195 2327 Planarity : 0.004 0.039 1513 Dihedral : 29.862 128.012 4375 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.50 % Allowed : 18.28 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.29), residues: 852 helix: 2.52 (0.22), residues: 553 sheet: -1.37 (1.02), residues: 28 loop : -0.98 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 47 TYR 0.030 0.002 TYR H 80 PHE 0.019 0.002 PHE K 32 TRP 0.024 0.009 TRP K 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 (14186) covalent geometry : angle 0.61667 / 0.36 (20485) hydrogen bonds : bond 0.05731 / 3.82 ( 790) hydrogen bonds : angle 3.09346 / 2.24 ( 1971) metal coordination : bond 0.01264 / 0.62 ( 4) metal coordination : angle 10.11927 / 3.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 265 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8526 (mmp80) cc_final: 0.7964 (mmm-85) REVERT: A 68 GLN cc_start: 0.8739 (tt0) cc_final: 0.8523 (tt0) REVERT: E 59 GLU cc_start: 0.7946 (pm20) cc_final: 0.7714 (pm20) REVERT: F 25 ASN cc_start: 0.8945 (m-40) cc_final: 0.8606 (m-40) REVERT: G 70 ARG cc_start: 0.9059 (tpp80) cc_final: 0.8746 (ttp-170) REVERT: K 47 ARG cc_start: 0.8282 (ttm110) cc_final: 0.7310 (mpp80) REVERT: M 45 PHE cc_start: 0.8285 (t80) cc_final: 0.7830 (t80) outliers start: 33 outliers final: 22 residues processed: 277 average time/residue: 0.1415 time to fit residues: 53.1592 Evaluate side-chains 265 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 31 GLN Chi-restraints excluded: chain M residue 55 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 2 GLN ** M 31 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 = 0.3538 r_free = 0.3538 target = 0.083652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.055580 restraints weight = 36964.469| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.63 r_work: 0.2737 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14190 Z= 0.154 Angle : 0.608 14.372 20491 Z= 0.353 Chirality : 0.040 0.194 2327 Planarity : 0.004 0.048 1513 Dihedral : 29.883 125.650 4375 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.68 % Allowed : 21.15 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.29), residues: 852 helix: 2.65 (0.22), residues: 549 sheet: -1.43 (0.98), residues: 28 loop : -0.93 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.034 0.002 TYR H 80 PHE 0.012 0.001 PHE K 32 TRP 0.008 0.002 TRP K 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (14186) covalent geometry : angle 0.59237 / 0.35 (20485) hydrogen bonds : bond 0.05312 / 3.55 ( 790) hydrogen bonds : angle 2.95306 / 2.16 ( 1971) metal coordination : bond 0.01100 / 0.54 ( 4) metal coordination : angle 7.94347 / 3.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 258 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8515 (mmp80) cc_final: 0.8209 (mmm-85) REVERT: D 32 GLU cc_start: 0.8300 (pt0) cc_final: 0.8074 (pt0) REVERT: E 42 ARG cc_start: 0.9010 (mtp180) cc_final: 0.8673 (mtp85) REVERT: F 25 ASN cc_start: 0.8917 (m110) cc_final: 0.8591 (m-40) REVERT: G 70 ARG cc_start: 0.9062 (tpp80) cc_final: 0.8774 (ttp-170) REVERT: K 47 ARG cc_start: 0.8565 (ttm110) cc_final: 0.8158 (mtm-85) REVERT: M 42 ARG cc_start: 0.7502 (ttm110) cc_final: 0.7113 (ttm110) REVERT: M 45 PHE cc_start: 0.8404 (t80) cc_final: 0.7917 (t80) outliers start: 27 outliers final: 21 residues processed: 272 average time/residue: 0.1354 time to fit residues: 50.5264 Evaluate side-chains 265 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 55 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 87 optimal weight: 50.0000 overall best weight: 6.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 18 ASN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 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 = 0.3453 r_free = 0.3453 target = 0.078850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.050690 restraints weight = 38347.713| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.76 r_work: 0.2615 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 14190 Z= 0.352 Angle : 0.812 13.664 20491 Z= 0.441 Chirality : 0.049 0.236 2327 Planarity : 0.006 0.067 1513 Dihedral : 30.211 126.128 4375 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 8.05 % Allowed : 17.74 % Favored : 74.22 % 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: 1.15 (0.28), residues: 852 helix: 1.82 (0.21), residues: 553 sheet: -1.21 (1.02), residues: 28 loop : -1.28 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 28 TYR 0.026 0.004 TYR D 80 PHE 0.018 0.003 PHE E 104 TRP 0.006 0.002 TRP K 25 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00750 / 0.35 (14186) covalent geometry : angle 0.80349 / 0.44 (20485) hydrogen bonds : bond 0.07817 / 5.24 ( 790) hydrogen bonds : angle 3.83257 / 2.78 ( 1971) metal coordination : bond 0.01825 / 0.90 ( 4) metal coordination : angle 6.79573 / 2.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 237 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 GLN cc_start: 0.9337 (OUTLIER) cc_final: 0.8991 (mp10) REVERT: F 84 MET cc_start: 0.8970 (mmp) cc_final: 0.8737 (mmp) REVERT: G 32 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9013 (mm) REVERT: H 40 LYS cc_start: 0.9383 (mtmt) cc_final: 0.9124 (ttmm) REVERT: K 40 LYS cc_start: 0.8231 (ttmm) cc_final: 0.7675 (tptm) REVERT: K 47 ARG cc_start: 0.8646 (ttm110) cc_final: 0.7689 (mpp80) REVERT: M 42 ARG cc_start: 0.7821 (ttm110) cc_final: 0.7404 (ttm110) REVERT: M 45 PHE cc_start: 0.8437 (t80) cc_final: 0.8028 (t80) outliers start: 59 outliers final: 46 residues processed: 268 average time/residue: 0.1326 time to fit residues: 48.6077 Evaluate side-chains 281 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 233 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 31 GLN Chi-restraints excluded: chain M residue 55 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.082334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.054011 restraints weight = 37126.157| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.65 r_work: 0.2709 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14190 Z= 0.148 Angle : 0.614 12.364 20491 Z= 0.357 Chirality : 0.040 0.198 2327 Planarity : 0.004 0.049 1513 Dihedral : 29.960 122.971 4375 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.46 % Allowed : 25.10 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.29), residues: 852 helix: 2.55 (0.22), residues: 548 sheet: -1.09 (1.03), residues: 28 loop : -1.02 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 33 TYR 0.016 0.002 TYR G 49 PHE 0.022 0.002 PHE K 32 TRP 0.003 0.001 TRP K 25 HIS 0.002 0.001 HIS C 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.15 (14186) covalent geometry : angle 0.60482 / 0.36 (20485) hydrogen bonds : bond 0.05409 / 3.66 ( 790) hydrogen bonds : angle 2.92622 / 2.11 ( 1971) metal coordination : bond 0.00902 / 0.44 ( 4) metal coordination : angle 6.31439 / 2.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 264 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ARG cc_start: 0.8746 (mtm110) cc_final: 0.8456 (ttm-80) REVERT: C 103 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.8903 (mp10) REVERT: E 42 ARG cc_start: 0.9095 (mtp180) cc_final: 0.8735 (mtp85) REVERT: E 120 MET cc_start: 0.8840 (mtm) cc_final: 0.8237 (mtm) REVERT: G 18 ASN cc_start: 0.9483 (t0) cc_final: 0.9247 (t0) REVERT: G 70 ARG cc_start: 0.9055 (tpp80) cc_final: 0.8774 (ttp-170) REVERT: H 40 LYS cc_start: 0.9346 (mtmt) cc_final: 0.9103 (ttmm) REVERT: K 40 LYS cc_start: 0.8365 (ttmm) cc_final: 0.7876 (tptm) REVERT: K 47 ARG cc_start: 0.8551 (ttm110) cc_final: 0.8141 (mtm-85) REVERT: M 42 ARG cc_start: 0.7756 (ttm110) cc_final: 0.7269 (ttm110) REVERT: M 45 PHE cc_start: 0.8402 (t80) cc_final: 0.7967 (t80) outliers start: 18 outliers final: 11 residues processed: 269 average time/residue: 0.1437 time to fit residues: 52.5949 Evaluate side-chains 257 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 245 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 31 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 7 optimal weight: 0.0040 chunk 44 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 17 optimal weight: 0.3980 overall best weight: 1.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.082325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.054326 restraints weight = 37278.059| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.63 r_work: 0.2718 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14190 Z= 0.152 Angle : 0.609 11.790 20491 Z= 0.354 Chirality : 0.040 0.199 2327 Planarity : 0.004 0.046 1513 Dihedral : 29.893 122.078 4375 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.00 % Allowed : 25.51 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.29), residues: 852 helix: 2.64 (0.22), residues: 548 sheet: -1.23 (1.02), residues: 28 loop : -0.96 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 33 TYR 0.023 0.002 TYR D 80 PHE 0.019 0.002 PHE K 32 TRP 0.020 0.005 TRP K 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (14186) covalent geometry : angle 0.60360 / 0.35 (20485) hydrogen bonds : bond 0.05210 / 3.51 ( 790) hydrogen bonds : angle 2.91996 / 2.11 ( 1971) metal coordination : bond 0.00878 / 0.43 ( 4) metal coordination : angle 4.95786 / 1.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ARG cc_start: 0.8749 (mtm110) cc_final: 0.8454 (ttm-80) REVERT: C 103 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8913 (mp10) REVERT: E 42 ARG cc_start: 0.9100 (mtp180) cc_final: 0.8777 (mtp85) REVERT: E 120 MET cc_start: 0.8849 (mtm) cc_final: 0.8228 (mtm) REVERT: F 25 ASN cc_start: 0.8923 (m-40) cc_final: 0.8596 (m-40) REVERT: G 18 ASN cc_start: 0.9497 (t0) cc_final: 0.9272 (t0) REVERT: G 70 ARG cc_start: 0.9051 (tpp80) cc_final: 0.8761 (ttp-170) REVERT: K 40 LYS cc_start: 0.8377 (ttmm) cc_final: 0.7929 (tptm) REVERT: K 47 ARG cc_start: 0.8448 (ttm110) cc_final: 0.8069 (mtm-85) REVERT: K 54 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8690 (pptt) REVERT: M 42 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7287 (ttm110) REVERT: M 45 PHE cc_start: 0.8418 (t80) cc_final: 0.7625 (t80) outliers start: 22 outliers final: 13 residues processed: 257 average time/residue: 0.1455 time to fit residues: 50.7780 Evaluate side-chains 252 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 43 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 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 = 0.3524 r_free = 0.3524 target = 0.082489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.054427 restraints weight = 37076.100| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.64 r_work: 0.2717 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14190 Z= 0.162 Angle : 0.613 11.781 20491 Z= 0.355 Chirality : 0.040 0.198 2327 Planarity : 0.004 0.041 1513 Dihedral : 29.885 121.094 4375 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.86 % Allowed : 25.24 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.29), residues: 852 helix: 2.66 (0.22), residues: 550 sheet: -1.08 (1.04), residues: 28 loop : -0.97 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 33 TYR 0.025 0.002 TYR B 88 PHE 0.016 0.001 PHE K 32 TRP 0.018 0.004 TRP K 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (14186) covalent geometry : angle 0.60913 / 0.35 (20485) hydrogen bonds : bond 0.05148 / 3.48 ( 790) hydrogen bonds : angle 2.90832 / 2.11 ( 1971) metal coordination : bond 0.00860 / 0.42 ( 4) metal coordination : angle 4.12374 / 1.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8013 (m-10) cc_final: 0.7801 (m-10) REVERT: C 34 ARG cc_start: 0.8776 (mtm110) cc_final: 0.8444 (ttm-80) REVERT: C 103 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.8879 (mp10) REVERT: E 42 ARG cc_start: 0.9095 (mtp180) cc_final: 0.8751 (mtp85) REVERT: E 94 GLU cc_start: 0.8894 (tp30) cc_final: 0.8661 (tp30) REVERT: F 25 ASN cc_start: 0.8910 (m-40) cc_final: 0.8580 (m-40) REVERT: G 18 ASN cc_start: 0.9504 (t0) cc_final: 0.9243 (t0) REVERT: G 70 ARG cc_start: 0.8974 (tpp80) cc_final: 0.8651 (ttp-170) REVERT: H 76 ARG cc_start: 0.9046 (ttp-110) cc_final: 0.8775 (ttp80) REVERT: K 40 LYS cc_start: 0.8385 (ttmm) cc_final: 0.7942 (tptm) REVERT: K 47 ARG cc_start: 0.8441 (ttm110) cc_final: 0.8061 (mtm-85) REVERT: K 54 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8686 (pptt) REVERT: M 45 PHE cc_start: 0.8402 (t80) cc_final: 0.7600 (t80) outliers start: 21 outliers final: 15 residues processed: 247 average time/residue: 0.1508 time to fit residues: 50.4057 Evaluate side-chains 251 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 235 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 43 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.6980 chunk 80 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 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 = 0.3526 r_free = 0.3526 target = 0.082624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.054673 restraints weight = 37405.189| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.66 r_work: 0.2724 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14190 Z= 0.159 Angle : 0.609 11.760 20491 Z= 0.353 Chirality : 0.040 0.198 2327 Planarity : 0.004 0.043 1513 Dihedral : 29.860 120.227 4375 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.27 % Allowed : 25.51 % Favored : 71.21 % 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: 2.21 (0.29), residues: 852 helix: 2.70 (0.22), residues: 550 sheet: -1.03 (1.05), residues: 28 loop : -0.94 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 33 TYR 0.030 0.002 TYR H 80 PHE 0.015 0.001 PHE K 32 TRP 0.020 0.005 TRP K 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (14186) covalent geometry : angle 0.60600 / 0.35 (20485) hydrogen bonds : bond 0.05028 / 3.40 ( 790) hydrogen bonds : angle 2.86058 / 2.08 ( 1971) metal coordination : bond 0.00797 / 0.39 ( 4) metal coordination : angle 3.51114 / 1.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8059 (m-10) cc_final: 0.7758 (m-10) REVERT: B 92 ARG cc_start: 0.9054 (ttp80) cc_final: 0.8778 (tmm-80) REVERT: C 34 ARG cc_start: 0.8782 (mtm110) cc_final: 0.8454 (ttm-80) REVERT: C 103 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.8855 (mp10) REVERT: D 32 GLU cc_start: 0.8871 (pt0) cc_final: 0.8320 (pt0) REVERT: E 42 ARG cc_start: 0.9110 (mtp180) cc_final: 0.8693 (mtp85) REVERT: E 94 GLU cc_start: 0.8892 (tp30) cc_final: 0.8608 (tp30) REVERT: G 18 ASN cc_start: 0.9516 (t0) cc_final: 0.9255 (t0) REVERT: H 40 LYS cc_start: 0.9350 (mtmt) cc_final: 0.9126 (ttmm) REVERT: H 76 ARG cc_start: 0.9111 (ttp-110) cc_final: 0.8787 (ttp80) REVERT: K 47 ARG cc_start: 0.8473 (ttm110) cc_final: 0.8104 (mtm-85) REVERT: K 54 LYS cc_start: 0.9059 (mmmt) cc_final: 0.8691 (pptt) REVERT: M 30 ILE cc_start: 0.8838 (mm) cc_final: 0.8623 (mm) REVERT: M 45 PHE cc_start: 0.8389 (t80) cc_final: 0.7561 (t80) outliers start: 24 outliers final: 19 residues processed: 252 average time/residue: 0.1453 time to fit residues: 49.6506 Evaluate side-chains 255 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 43 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 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 = 0.3530 r_free = 0.3530 target = 0.082841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.054804 restraints weight = 37319.600| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.65 r_work: 0.2733 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14190 Z= 0.155 Angle : 0.609 11.968 20491 Z= 0.353 Chirality : 0.040 0.196 2327 Planarity : 0.004 0.032 1513 Dihedral : 29.834 119.486 4375 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.86 % Allowed : 25.78 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.29), residues: 852 helix: 2.76 (0.22), residues: 549 sheet: -1.17 (1.02), residues: 28 loop : -0.89 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 33 TYR 0.026 0.002 TYR H 80 PHE 0.020 0.002 PHE K 32 TRP 0.019 0.005 TRP K 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (14186) covalent geometry : angle 0.60621 / 0.35 (20485) hydrogen bonds : bond 0.04922 / 3.33 ( 790) hydrogen bonds : angle 2.83928 / 2.05 ( 1971) metal coordination : bond 0.00781 / 0.38 ( 4) metal coordination : angle 3.52648 / 1.42 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8069 (m-10) cc_final: 0.7814 (m-10) REVERT: B 92 ARG cc_start: 0.9047 (ttp80) cc_final: 0.8786 (tmm-80) REVERT: C 34 ARG cc_start: 0.8772 (mtm110) cc_final: 0.8443 (ttm-80) REVERT: C 103 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.8902 (mp10) REVERT: E 42 ARG cc_start: 0.9107 (mtp180) cc_final: 0.8690 (mtp85) REVERT: F 25 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8691 (m-40) REVERT: G 18 ASN cc_start: 0.9504 (t0) cc_final: 0.9239 (t0) REVERT: G 70 ARG cc_start: 0.9059 (tpp80) cc_final: 0.8673 (ttp80) REVERT: H 40 LYS cc_start: 0.9356 (mtmt) cc_final: 0.9134 (ttmm) REVERT: H 76 ARG cc_start: 0.9106 (ttp-110) cc_final: 0.8792 (ttp80) REVERT: K 47 ARG cc_start: 0.8466 (ttm110) cc_final: 0.8104 (mtm-85) REVERT: K 54 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8627 (pptt) REVERT: M 30 ILE cc_start: 0.8827 (mm) cc_final: 0.8622 (mm) REVERT: M 45 PHE cc_start: 0.8374 (t80) cc_final: 0.7528 (t80) outliers start: 21 outliers final: 18 residues processed: 250 average time/residue: 0.1527 time to fit residues: 51.3471 Evaluate side-chains 258 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 2 GLN Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 43 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 8 optimal weight: 0.0000 chunk 103 optimal weight: 30.0000 chunk 65 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 2 GLN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 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 = 0.3537 r_free = 0.3537 target = 0.083209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.055202 restraints weight = 37343.216| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.65 r_work: 0.2742 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14190 Z= 0.147 Angle : 0.605 12.392 20491 Z= 0.351 Chirality : 0.039 0.194 2327 Planarity : 0.004 0.041 1513 Dihedral : 29.816 118.989 4375 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.86 % Allowed : 25.78 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.29), residues: 852 helix: 2.80 (0.22), residues: 549 sheet: -1.22 (1.01), residues: 28 loop : -0.87 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 96 TYR 0.024 0.002 TYR H 80 PHE 0.017 0.002 PHE K 32 TRP 0.014 0.003 TRP K 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 (14186) covalent geometry : angle 0.60260 / 0.35 (20485) hydrogen bonds : bond 0.04824 / 3.26 ( 790) hydrogen bonds : angle 2.80501 / 2.03 ( 1971) metal coordination : bond 0.00692 / 0.34 ( 4) metal coordination : angle 3.19768 / 1.33 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3756.09 seconds wall clock time: 64 minutes 42.57 seconds (3882.57 seconds total)