Starting phenix.real_space_refine on Thu Aug 6 01:47:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pp6_17796/08_2026/8pp6_17796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pp6_17796/08_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_17796/08_2026/8pp6_17796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pp6_17796/08_2026/8pp6_17796.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pp6_17796/08_2026/8pp6_17796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pp6_17796/08_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-2.2rc3-6140/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: 2.99, per 1000 atoms: 0.22 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: 0.96 Conformation dependent library (CDL) restraints added in 385.0 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: 1.88 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: 2.42 Time building geometry restraints manager: 1.36 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: 18070 1.10 - 2.20: 1879 2.20 - 3.29: 511 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: 0.750 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.450 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.830 ------------------------------------------------------------------------------- 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 : 0.740 13.065 20491 Z= 0.640 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 0.72761 / 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 : 0.314 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: E 79 LYS cc_start: 0.7642 (tttp) cc_final: 0.7430 (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: 0.1554 time to fit residues: 66.1089 Evaluate side-chains 254 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.084856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.056382 restraints weight = 36539.561| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.71 r_work: 0.2746 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14190 Z= 0.163 Angle : 0.718 23.917 20491 Z= 0.395 Chirality : 0.044 0.191 2327 Planarity : 0.005 0.055 1513 Dihedral : 29.441 131.936 4377 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: 1.92 (0.29), residues: 852 helix: 2.41 (0.22), residues: 548 sheet: -0.85 (1.03), residues: 28 loop : -0.90 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 33 TYR 0.030 0.003 TYR H 80 PHE 0.016 0.002 PHE K 39 TRP 0.009 0.002 TRP K 25 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.16 (14186) covalent geometry : angle 0.67419 / 0.39 (20485) hydrogen bonds : bond 0.06303 / 4.24 ( 790) hydrogen bonds : angle 3.22161 / 2.34 ( 1971) metal coordination : bond 0.03154 / 1.60 ( 4) metal coordination : angle 14.39322 / 6.17 ( 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 301 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 277 time to evaluate : 0.322 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 79 LYS cc_start: 0.8476 (tptm) cc_final: 0.8164 (tptm) REVERT: B 43 VAL cc_start: 0.8986 (t) cc_final: 0.8750 (m) REVERT: B 74 GLU cc_start: 0.9271 (tt0) cc_final: 0.9013 (tp30) REVERT: D 32 GLU cc_start: 0.8454 (pt0) cc_final: 0.8183 (pt0) REVERT: E 42 ARG cc_start: 0.8949 (mtp180) cc_final: 0.8598 (mtp85) REVERT: E 59 GLU cc_start: 0.7941 (pm20) cc_final: 0.7644 (pm20) REVERT: M 4 PHE cc_start: 0.5612 (m-80) cc_final: 0.5320 (m-80) REVERT: M 45 PHE cc_start: 0.8242 (t80) cc_final: 0.7852 (t80) outliers start: 24 outliers final: 15 residues processed: 285 average time/residue: 0.1263 time to fit residues: 49.6798 Evaluate side-chains 273 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 258 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 C residue 15 SER Chi-restraints excluded: chain C residue 88 ASN 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 50 ILE Chi-restraints excluded: chain F residue 82 THR 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: 0.9990 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 25 ASN G 18 ASN G 83 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.082100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.053548 restraints weight = 37241.114| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.70 r_work: 0.2684 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14190 Z= 0.214 Angle : 0.696 20.545 20491 Z= 0.384 Chirality : 0.044 0.207 2327 Planarity : 0.005 0.041 1513 Dihedral : 29.891 129.437 4375 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.18 % Allowed : 18.42 % Favored : 76.40 % 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: 1.83 (0.29), residues: 852 helix: 2.41 (0.22), residues: 552 sheet: -0.89 (1.32), residues: 17 loop : -1.18 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 47 TYR 0.020 0.003 TYR H 80 PHE 0.019 0.002 PHE K 32 TRP 0.029 0.009 TRP K 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.21 (14186) covalent geometry : angle 0.66966 / 0.38 (20485) hydrogen bonds : bond 0.06334 / 4.23 ( 790) hydrogen bonds : angle 3.23942 / 2.34 ( 1971) metal coordination : bond 0.01689 / 0.82 ( 4) metal coordination : angle 11.10542 / 4.20 ( 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: 38 poor density : 260 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: B 88 TYR cc_start: 0.8780 (m-10) cc_final: 0.8284 (m-10) REVERT: D 32 GLU cc_start: 0.8404 (pt0) cc_final: 0.8079 (pt0) REVERT: E 42 ARG cc_start: 0.9003 (mtp180) cc_final: 0.8671 (mtp85) REVERT: E 59 GLU cc_start: 0.8186 (pm20) cc_final: 0.7839 (pm20) REVERT: E 94 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8476 (tt0) REVERT: F 25 ASN cc_start: 0.9154 (m110) cc_final: 0.8762 (m-40) REVERT: F 43 VAL cc_start: 0.9033 (t) cc_final: 0.8799 (m) REVERT: G 32 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9099 (mm) REVERT: G 70 ARG cc_start: 0.9086 (tpp80) cc_final: 0.8748 (ttp-170) REVERT: K 47 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7259 (mpp80) REVERT: M 45 PHE cc_start: 0.8283 (t80) cc_final: 0.7821 (t80) outliers start: 38 outliers final: 26 residues processed: 274 average time/residue: 0.1383 time to fit residues: 51.8670 Evaluate side-chains 271 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 243 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 73 THR Chi-restraints excluded: chain C residue 29 ILE 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 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 E residue 101 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 110 ILE 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 K residue 47 ARG Chi-restraints excluded: chain M residue 50 LEU 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: 20.0000 chunk 18 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 0.0770 chunk 12 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN ** K 34 ASN ** 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 = 0.3547 r_free = 0.3547 target = 0.084043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.056023 restraints weight = 36795.297| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.68 r_work: 0.2751 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14190 Z= 0.142 Angle : 0.604 14.870 20491 Z= 0.349 Chirality : 0.040 0.197 2327 Planarity : 0.004 0.057 1513 Dihedral : 29.805 125.226 4375 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.86 % Allowed : 21.96 % 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: 2.20 (0.29), residues: 852 helix: 2.72 (0.22), residues: 548 sheet: -1.27 (1.01), residues: 28 loop : -0.93 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 33 TYR 0.020 0.002 TYR G 56 PHE 0.015 0.002 PHE K 39 TRP 0.007 0.002 TRP K 25 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.14 (14186) covalent geometry : angle 0.58904 / 0.35 (20485) hydrogen bonds : bond 0.05071 / 3.42 ( 790) hydrogen bonds : angle 2.83249 / 2.05 ( 1971) metal coordination : bond 0.00933 / 0.46 ( 4) metal coordination : angle 7.77598 / 2.91 ( 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 290 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 269 time to evaluate : 0.361 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: symmetry clash REVERT: D 32 GLU cc_start: 0.8320 (pt0) cc_final: 0.7948 (pt0) REVERT: E 42 ARG cc_start: 0.8997 (mtp180) cc_final: 0.8668 (mtp85) REVERT: E 59 GLU cc_start: 0.8015 (pm20) cc_final: 0.7490 (pm20) REVERT: E 61 LEU cc_start: 0.9279 (mt) cc_final: 0.9074 (mp) REVERT: E 94 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8409 (tt0) REVERT: F 25 ASN cc_start: 0.9067 (m110) cc_final: 0.8736 (m-40) REVERT: F 84 MET cc_start: 0.8910 (mmp) cc_final: 0.8683 (mmp) REVERT: F 92 ARG cc_start: 0.9050 (ttp80) cc_final: 0.8833 (ttp80) REVERT: G 32 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9121 (mm) REVERT: G 70 ARG cc_start: 0.9051 (tpp80) cc_final: 0.8759 (ttp-170) REVERT: H 102 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8261 (mm-30) REVERT: K 47 ARG cc_start: 0.8460 (ttm110) cc_final: 0.7957 (mtm110) REVERT: M 42 ARG cc_start: 0.7844 (ttm110) cc_final: 0.6816 (mpp80) REVERT: M 45 PHE cc_start: 0.8416 (t80) cc_final: 0.7952 (t80) outliers start: 21 outliers final: 13 residues processed: 276 average time/residue: 0.1394 time to fit residues: 52.8729 Evaluate side-chains 272 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 258 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 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 F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 86 ILE 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: 1.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 87 optimal weight: 50.0000 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 ASN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 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 = 0.3457 r_free = 0.3457 target = 0.079145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.051268 restraints weight = 37822.320| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.69 r_work: 0.2624 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 14190 Z= 0.350 Angle : 0.794 13.457 20491 Z= 0.433 Chirality : 0.048 0.228 2327 Planarity : 0.006 0.059 1513 Dihedral : 30.085 126.309 4375 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 6.96 % Allowed : 20.19 % Favored : 72.85 % 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: 1.38 (0.28), residues: 852 helix: 2.03 (0.22), residues: 554 sheet: -1.33 (0.99), residues: 28 loop : -1.25 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 83 TYR 0.024 0.003 TYR D 80 PHE 0.014 0.002 PHE E 104 TRP 0.009 0.003 TRP K 25 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.35 (14186) covalent geometry : angle 0.78487 / 0.43 (20485) hydrogen bonds : bond 0.07429 / 4.98 ( 790) hydrogen bonds : angle 3.64755 / 2.64 ( 1971) metal coordination : bond 0.01666 / 0.82 ( 4) metal coordination : angle 7.07383 / 2.67 ( 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 292 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 241 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 GLU cc_start: 0.8403 (pt0) cc_final: 0.8192 (pt0) REVERT: G 32 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9097 (mm) REVERT: K 40 LYS cc_start: 0.8190 (ttmm) cc_final: 0.7680 (tptm) REVERT: K 47 ARG cc_start: 0.8508 (ttm110) cc_final: 0.8058 (mtm-85) REVERT: K 54 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8699 (pptt) REVERT: M 42 ARG cc_start: 0.7910 (ttm110) cc_final: 0.7563 (ttm110) REVERT: M 45 PHE cc_start: 0.8426 (t80) cc_final: 0.8024 (t80) outliers start: 51 outliers final: 43 residues processed: 269 average time/residue: 0.1383 time to fit residues: 50.9657 Evaluate side-chains 277 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 233 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 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 75 THR Chi-restraints excluded: chain C residue 90 GLU 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 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 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 49 THR 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 26 VAL Chi-restraints excluded: chain M residue 30 ILE 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: 2.9990 chunk 76 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.082154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.053921 restraints weight = 37133.991| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.64 r_work: 0.2707 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2782 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= 0.151 Angle : 0.619 12.573 20491 Z= 0.359 Chirality : 0.041 0.200 2327 Planarity : 0.004 0.055 1513 Dihedral : 29.904 124.002 4375 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.05 % Allowed : 25.78 % Favored : 72.17 % 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: 2.05 (0.29), residues: 852 helix: 2.64 (0.22), residues: 547 sheet: -1.26 (1.03), residues: 28 loop : -1.09 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 70 TYR 0.024 0.002 TYR D 80 PHE 0.023 0.002 PHE K 32 TRP 0.006 0.002 TRP K 25 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (14186) covalent geometry : angle 0.60930 / 0.36 (20485) hydrogen bonds : bond 0.05411 / 3.66 ( 790) hydrogen bonds : angle 2.93089 / 2.12 ( 1971) metal coordination : bond 0.00914 / 0.45 ( 4) metal coordination : angle 6.39616 / 2.43 ( 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 273 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 258 time to evaluate : 0.361 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: 0.8759 (mtm110) cc_final: 0.8451 (ttm-80) REVERT: D 32 GLU cc_start: 0.8285 (pt0) cc_final: 0.7840 (pt0) REVERT: E 42 ARG cc_start: 0.9076 (mtp180) cc_final: 0.8750 (mtp85) REVERT: E 94 GLU cc_start: 0.8900 (tp30) cc_final: 0.8600 (mt-10) REVERT: E 120 MET cc_start: 0.8851 (mtm) cc_final: 0.8323 (mtm) REVERT: F 25 ASN cc_start: 0.9100 (m-40) cc_final: 0.8560 (m-40) REVERT: G 18 ASN cc_start: 0.9492 (t0) cc_final: 0.9232 (t0) REVERT: G 32 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9119 (mm) REVERT: G 70 ARG cc_start: 0.9090 (tpp80) cc_final: 0.8795 (ttp-170) REVERT: H 40 LYS cc_start: 0.9366 (mtmt) cc_final: 0.9132 (ttmm) REVERT: H 102 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8420 (mm-30) REVERT: K 40 LYS cc_start: 0.8225 (ttmm) cc_final: 0.7683 (tptt) REVERT: K 47 ARG cc_start: 0.8347 (ttm110) cc_final: 0.8098 (mtm-85) REVERT: K 54 LYS cc_start: 0.9029 (mmmt) cc_final: 0.8719 (pptt) REVERT: M 43 LEU cc_start: 0.8948 (mm) cc_final: 0.8479 (pt) REVERT: M 45 PHE cc_start: 0.8362 (t80) cc_final: 0.7971 (t80) outliers start: 15 outliers final: 10 residues processed: 264 average time/residue: 0.1414 time to fit residues: 50.7992 Evaluate side-chains 260 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 249 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 113 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain H residue 84 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 0.0770 chunk 6 optimal weight: 0.9990 chunk 62 optimal weight: 0.0050 chunk 7 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 chunk 17 optimal weight: 0.0770 overall best weight: 0.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN K 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.084010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.055963 restraints weight = 37236.702| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.66 r_work: 0.2760 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2960 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= 0.136 Angle : 0.593 11.680 20491 Z= 0.347 Chirality : 0.039 0.195 2327 Planarity : 0.004 0.038 1513 Dihedral : 29.723 122.193 4375 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.91 % Allowed : 26.19 % 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: 2.40 (0.30), residues: 852 helix: 2.88 (0.22), residues: 547 sheet: -1.38 (1.03), residues: 28 loop : -0.85 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 33 TYR 0.027 0.002 TYR B 88 PHE 0.018 0.001 PHE K 32 TRP 0.017 0.004 TRP K 25 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.14 (14186) covalent geometry : angle 0.58906 / 0.35 (20485) hydrogen bonds : bond 0.04677 / 3.15 ( 790) hydrogen bonds : angle 2.72613 / 1.97 ( 1971) metal coordination : bond 0.00671 / 0.33 ( 4) metal coordination : angle 4.20654 / 1.64 ( 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 272 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 258 time to evaluate : 0.354 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: C 34 ARG cc_start: 0.8752 (mtm110) cc_final: 0.8495 (ttm-80) REVERT: E 42 ARG cc_start: 0.9075 (mtp180) cc_final: 0.8756 (mtp85) REVERT: E 120 MET cc_start: 0.8806 (mtm) cc_final: 0.8261 (mtm) REVERT: G 18 ASN cc_start: 0.9505 (t0) cc_final: 0.9219 (t0) REVERT: G 32 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9129 (mm) REVERT: G 70 ARG cc_start: 0.8965 (tpp80) cc_final: 0.8632 (ttp-170) REVERT: K 47 ARG cc_start: 0.8391 (ttm110) cc_final: 0.7900 (mtm-85) REVERT: K 54 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8732 (pptt) REVERT: M 43 LEU cc_start: 0.8890 (mm) cc_final: 0.8302 (pt) REVERT: M 45 PHE cc_start: 0.8348 (t80) cc_final: 0.7569 (t80) outliers start: 14 outliers final: 10 residues processed: 264 average time/residue: 0.1442 time to fit residues: 52.0226 Evaluate side-chains 254 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 243 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain H residue 84 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 110 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.082999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.055224 restraints weight = 36872.630| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.62 r_work: 0.2739 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14190 Z= 0.163 Angle : 0.620 11.298 20491 Z= 0.356 Chirality : 0.040 0.198 2327 Planarity : 0.004 0.038 1513 Dihedral : 29.786 122.037 4375 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.86 % Allowed : 26.60 % Favored : 70.53 % 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: 2.23 (0.29), residues: 852 helix: 2.72 (0.22), residues: 554 sheet: -1.19 (1.03), residues: 28 loop : -0.97 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 33 TYR 0.018 0.002 TYR B 88 PHE 0.016 0.002 PHE E 67 TRP 0.010 0.003 TRP K 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (14186) covalent geometry : angle 0.61701 / 0.36 (20485) hydrogen bonds : bond 0.04956 / 3.34 ( 790) hydrogen bonds : angle 2.82835 / 2.05 ( 1971) metal coordination : bond 0.00764 / 0.38 ( 4) metal coordination : angle 3.68841 / 1.43 ( 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 262 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 0.281 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: C 34 ARG cc_start: 0.8765 (mtm110) cc_final: 0.8422 (ttm-80) REVERT: C 103 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.8843 (mp10) REVERT: E 42 ARG cc_start: 0.9052 (mtp180) cc_final: 0.8725 (mtp85) REVERT: E 94 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8273 (tt0) REVERT: E 120 MET cc_start: 0.8876 (mtm) cc_final: 0.8292 (mtm) REVERT: F 25 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8601 (m-40) REVERT: G 18 ASN cc_start: 0.9515 (t0) cc_final: 0.9232 (t0) REVERT: G 32 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9159 (mm) REVERT: K 47 ARG cc_start: 0.8460 (ttm110) cc_final: 0.8001 (mtm-85) REVERT: M 43 LEU cc_start: 0.8889 (mm) cc_final: 0.8318 (pt) REVERT: M 45 PHE cc_start: 0.8351 (t80) cc_final: 0.7548 (t80) outliers start: 21 outliers final: 15 residues processed: 247 average time/residue: 0.1462 time to fit residues: 49.1810 Evaluate side-chains 254 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 236 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 95 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.083477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.055495 restraints weight = 37500.334| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.67 r_work: 0.2747 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14190 Z= 0.151 Angle : 0.614 11.356 20491 Z= 0.357 Chirality : 0.039 0.193 2327 Planarity : 0.004 0.045 1513 Dihedral : 29.771 121.615 4375 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.59 % Allowed : 26.74 % Favored : 70.67 % 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: 2.31 (0.29), residues: 852 helix: 2.78 (0.22), residues: 553 sheet: -1.21 (1.02), residues: 28 loop : -0.93 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 33 TYR 0.031 0.002 TYR B 88 PHE 0.019 0.002 PHE K 39 TRP 0.008 0.002 TRP K 25 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (14186) covalent geometry : angle 0.61155 / 0.36 (20485) hydrogen bonds : bond 0.04830 / 3.27 ( 790) hydrogen bonds : angle 2.78147 / 2.01 ( 1971) metal coordination : bond 0.00655 / 0.32 ( 4) metal coordination : angle 3.53100 / 1.37 ( 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 260 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 0.337 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: 0.8774 (mtm110) cc_final: 0.8449 (ttm-80) REVERT: C 103 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8846 (mp10) REVERT: D 32 GLU cc_start: 0.8343 (pt0) cc_final: 0.8051 (pt0) REVERT: E 42 ARG cc_start: 0.9054 (mtp180) cc_final: 0.8729 (mtp85) REVERT: E 94 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8279 (tt0) REVERT: E 120 MET cc_start: 0.8858 (mtm) cc_final: 0.8287 (mtm) REVERT: F 25 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8630 (m-40) REVERT: G 18 ASN cc_start: 0.9516 (t0) cc_final: 0.9235 (t0) REVERT: G 32 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9176 (mm) REVERT: G 70 ARG cc_start: 0.8956 (tpp80) cc_final: 0.8735 (ttp-170) REVERT: K 47 ARG cc_start: 0.8434 (ttm110) cc_final: 0.7979 (mtm-85) REVERT: K 54 LYS cc_start: 0.8997 (mmmt) cc_final: 0.8704 (pptt) REVERT: M 43 LEU cc_start: 0.8894 (mm) cc_final: 0.8305 (pt) REVERT: M 45 PHE cc_start: 0.8338 (t80) cc_final: 0.7542 (t80) outliers start: 19 outliers final: 12 residues processed: 248 average time/residue: 0.1468 time to fit residues: 49.5222 Evaluate side-chains 253 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 238 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain H residue 84 SER 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: 2.9990 chunk 2 optimal weight: 8.9990 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: 2.9990 chunk 44 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.082652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.054657 restraints weight = 37497.799| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.64 r_work: 0.2728 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14190 Z= 0.180 Angle : 0.634 11.558 20491 Z= 0.364 Chirality : 0.040 0.195 2327 Planarity : 0.004 0.053 1513 Dihedral : 29.794 121.821 4375 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.86 % Allowed : 26.60 % Favored : 70.53 % 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: 2.23 (0.29), residues: 852 helix: 2.73 (0.22), residues: 555 sheet: -1.18 (1.01), residues: 28 loop : -1.02 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 33 TYR 0.019 0.002 TYR G 56 PHE 0.015 0.002 PHE K 39 TRP 0.007 0.002 TRP K 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 (14186) covalent geometry : angle 0.63164 / 0.36 (20485) hydrogen bonds : bond 0.05050 / 3.42 ( 790) hydrogen bonds : angle 2.87945 / 2.08 ( 1971) metal coordination : bond 0.00793 / 0.39 ( 4) metal coordination : angle 3.48322 / 1.36 ( 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 261 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 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: C 34 ARG cc_start: 0.8759 (mtm110) cc_final: 0.8407 (ttm-80) REVERT: C 103 GLN cc_start: 0.9346 (OUTLIER) cc_final: 0.8866 (mp10) REVERT: D 32 GLU cc_start: 0.8366 (pt0) cc_final: 0.8082 (pt0) REVERT: E 42 ARG cc_start: 0.9063 (mtp180) cc_final: 0.8738 (mtp85) REVERT: E 94 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8307 (tt0) REVERT: F 25 ASN cc_start: 0.9174 (OUTLIER) cc_final: 0.8809 (m-40) REVERT: G 18 ASN cc_start: 0.9518 (t0) cc_final: 0.9241 (t0) REVERT: G 32 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9153 (mm) REVERT: G 70 ARG cc_start: 0.9137 (tpp80) cc_final: 0.8913 (ttp-170) REVERT: H 102 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8293 (mm-30) REVERT: K 33 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.7924 (mmm-85) REVERT: K 47 ARG cc_start: 0.8429 (ttm110) cc_final: 0.7973 (mtm-85) REVERT: M 43 LEU cc_start: 0.8895 (mm) cc_final: 0.8322 (pt) REVERT: M 45 PHE cc_start: 0.8405 (t80) cc_final: 0.7575 (t80) outliers start: 21 outliers final: 15 residues processed: 248 average time/residue: 0.1498 time to fit residues: 50.2273 Evaluate side-chains 255 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER 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 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER 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 F residue 54 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain H residue 84 SER 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: 0.9980 chunk 50 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** 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 = 0.3534 r_free = 0.3534 target = 0.083011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.054966 restraints weight = 37383.997| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.68 r_work: 0.2735 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14190 Z= 0.161 Angle : 0.624 11.756 20491 Z= 0.359 Chirality : 0.040 0.193 2327 Planarity : 0.004 0.047 1513 Dihedral : 29.786 121.562 4375 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.73 % Allowed : 26.60 % Favored : 70.67 % 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: 2.23 (0.29), residues: 852 helix: 2.73 (0.22), residues: 555 sheet: -1.23 (1.00), residues: 28 loop : -1.01 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 33 TYR 0.018 0.002 TYR G 56 PHE 0.014 0.002 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 0.00301 / 0.16 (14186) covalent geometry : angle 0.62118 / 0.36 (20485) hydrogen bonds : bond 0.04972 / 3.37 ( 790) hydrogen bonds : angle 2.83526 / 2.05 ( 1971) metal coordination : bond 0.00734 / 0.36 ( 4) metal coordination : angle 3.39812 / 1.46 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3926.08 seconds wall clock time: 67 minutes 33.64 seconds (4053.64 seconds total)