Starting phenix.real_space_refine on Sat Aug 23 15:00:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pp6_17796/08_2025/8pp6_17796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pp6_17796/08_2025/8pp6_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_2025/8pp6_17796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pp6_17796/08_2025/8pp6_17796.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pp6_17796/08_2025/8pp6_17796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pp6_17796/08_2025/8pp6_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-2.0-5787/lib/python3.9/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: 2.93, 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: 1.03 Conformation dependent library (CDL) restraints added in 364.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.34 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: 2.55 Time building geometry restraints manager: 1.41 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=" CB THR F 71 " pdb=" CG2 THR F 71 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.37e+00 bond pdb=" C4' DC I 70 " pdb=" O4' DC I 70 " ideal model delta sigma weight residual 1.450 1.428 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C3' DT J 14 " pdb=" C2' DT J 14 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" O4' DC I 10 " pdb=" C1' DC I 10 " ideal model delta sigma weight residual 1.414 1.394 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" O4' DT J 9 " pdb=" C1' DT J 9 " ideal model delta sigma weight residual 1.414 1.395 0.019 2.00e-02 2.50e+03 9.30e-01 ... (remaining 14181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 19277 1.10 - 2.20: 973 2.20 - 3.29: 213 3.29 - 4.39: 13 4.39 - 5.49: 9 Bond angle restraints: 20485 Sorted by residual: angle pdb=" N THR K 31 " pdb=" CA THR K 31 " pdb=" CB THR K 31 " ideal model delta sigma weight residual 113.65 109.91 3.74 1.47e+00 4.63e-01 6.46e+00 angle pdb=" N THR K 31 " pdb=" CA THR K 31 " pdb=" C THR K 31 " ideal model delta sigma weight residual 113.72 110.04 3.68 1.52e+00 4.33e-01 5.85e+00 angle pdb=" C3' DC I 5 " pdb=" C2' DC I 5 " pdb=" C1' DC I 5 " ideal model delta sigma weight residual 101.60 98.07 3.53 1.50e+00 4.44e-01 5.55e+00 angle pdb=" CB LYS K 54 " pdb=" CG LYS K 54 " pdb=" CD LYS K 54 " ideal model delta sigma weight residual 111.30 116.27 -4.97 2.30e+00 1.89e-01 4.67e+00 angle pdb=" C VAL F 70 " pdb=" N THR F 71 " pdb=" CA THR F 71 " ideal model delta sigma weight residual 120.31 117.16 3.15 1.52e+00 4.33e-01 4.28e+00 ... (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 - 0.025: 1295 0.025 - 0.049: 711 0.049 - 0.074: 224 0.074 - 0.099: 56 0.099 - 0.123: 41 Chirality restraints: 2327 Sorted by residual: chirality pdb=" CA ILE G 78 " pdb=" N ILE G 78 " pdb=" C ILE G 78 " pdb=" CB ILE G 78 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA PRO D 47 " pdb=" N PRO D 47 " pdb=" C PRO D 47 " pdb=" CB PRO D 47 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.61e-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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.020 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14190 Z= 0.204 Angle : 0.579 13.065 20491 Z= 0.338 Chirality : 0.035 0.123 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 aren 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 covalent geometry : bond 0.00454 (14186) covalent geometry : angle 0.56294 (20485) hydrogen bonds : bond 0.13402 ( 790) hydrogen bonds : angle 3.74001 ( 1971) metal coordination : bond 0.00683 ( 4) metal coordination : angle 7.86947 ( 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 : 0.273 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: 0.1532 time to fit residues: 64.3878 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 : 0.367 ------------------------------------------------------------------------------- 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: 7.9990 chunk 53 optimal weight: 0.0870 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: 7.9990 chunk 106 optimal weight: 30.0000 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 68 GLN F 93 GLN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS G 83 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.084880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.056826 restraints weight = 36767.108| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.70 r_work: 0.2761 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14190 Z= 0.163 Angle : 0.591 15.496 20491 Z= 0.338 Chirality : 0.034 0.137 2327 Planarity : 0.004 0.033 1513 Dihedral : 29.333 131.655 4377 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.73 % Allowed : 18.14 % Favored : 79.13 % 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 aren not related in a simple way. whole: 2.21 (0.29), residues: 852 helix: 2.67 (0.22), residues: 548 sheet: -0.60 (1.34), residues: 17 loop : -0.89 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 63 TYR 0.022 0.002 TYR D 80 PHE 0.016 0.002 PHE K 39 TRP 0.014 0.003 TRP K 25 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00347 (14186) covalent geometry : angle 0.56535 (20485) hydrogen bonds : bond 0.05003 ( 790) hydrogen bonds : angle 2.91558 ( 1971) metal coordination : bond 0.00943 ( 4) metal coordination : angle 10.16503 ( 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 308 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 288 time to evaluate : 0.359 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: 0.8461 (mmp80) cc_final: 0.7947 (mmm-85) REVERT: A 68 GLN cc_start: 0.8766 (tt0) cc_final: 0.8563 (tt0) REVERT: A 99 TYR cc_start: 0.8909 (t80) cc_final: 0.8703 (t80) REVERT: B 88 TYR cc_start: 0.8683 (m-10) cc_final: 0.8470 (m-10) REVERT: D 32 GLU cc_start: 0.8388 (pt0) cc_final: 0.8123 (pt0) REVERT: E 59 GLU cc_start: 0.7894 (pm20) cc_final: 0.7435 (pm20) REVERT: E 120 MET cc_start: 0.8745 (mtm) cc_final: 0.8184 (mtm) REVERT: F 25 ASN cc_start: 0.8972 (m-40) cc_final: 0.8663 (m-40) REVERT: M 45 PHE cc_start: 0.8388 (t80) cc_final: 0.7847 (t80) outliers start: 20 outliers final: 12 residues processed: 294 average time/residue: 0.1381 time to fit residues: 55.5326 Evaluate side-chains 263 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 251 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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 115 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain H residue 119 THR 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: 3.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.082273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.054047 restraints weight = 37412.884| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.65 r_work: 0.2707 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14190 Z= 0.216 Angle : 0.590 11.330 20491 Z= 0.342 Chirality : 0.035 0.125 2327 Planarity : 0.004 0.036 1513 Dihedral : 29.363 131.149 4375 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.23 % Allowed : 19.37 % 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 aren not related in a simple way. whole: 2.20 (0.29), residues: 852 helix: 2.69 (0.22), residues: 552 sheet: -1.09 (1.04), residues: 28 loop : -0.96 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 47 TYR 0.042 0.002 TYR H 80 PHE 0.015 0.002 PHE K 32 TRP 0.003 0.001 TRP K 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00480 (14186) covalent geometry : angle 0.57796 (20485) hydrogen bonds : bond 0.05152 ( 790) hydrogen bonds : angle 2.97303 ( 1971) metal coordination : bond 0.00937 ( 4) metal coordination : angle 6.88016 ( 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 282 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 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: A 63 ARG cc_start: 0.8571 (mmp80) cc_final: 0.8008 (mmm-85) REVERT: B 88 TYR cc_start: 0.8941 (m-10) cc_final: 0.8691 (m-10) REVERT: D 32 GLU cc_start: 0.8248 (pt0) cc_final: 0.7896 (pt0) REVERT: E 42 ARG cc_start: 0.9044 (mtp180) cc_final: 0.8688 (mtp85) REVERT: E 120 MET cc_start: 0.8888 (mtm) cc_final: 0.8305 (mtm) REVERT: F 25 ASN cc_start: 0.8963 (m-40) cc_final: 0.8629 (m-40) REVERT: G 32 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9093 (mm) REVERT: H 102 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8342 (mm-30) REVERT: K 48 LYS cc_start: 0.8542 (tttp) cc_final: 0.8156 (tttm) REVERT: M 42 ARG cc_start: 0.7599 (ttm110) cc_final: 0.7253 (ttm110) REVERT: M 45 PHE cc_start: 0.8398 (t80) cc_final: 0.8140 (t80) outliers start: 31 outliers final: 25 residues processed: 265 average time/residue: 0.1447 time to fit residues: 51.6026 Evaluate side-chains 263 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 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 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 D residue 119 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU 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 71 ASP Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 30.0000 chunk 18 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 62 optimal weight: 0.0570 chunk 35 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 overall best weight: 2.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3526 r_free = 0.3526 target = 0.082784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.054606 restraints weight = 37246.562| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.63 r_work: 0.2719 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14190 Z= 0.189 Angle : 0.563 11.184 20491 Z= 0.330 Chirality : 0.033 0.126 2327 Planarity : 0.004 0.033 1513 Dihedral : 29.237 130.012 4375 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.82 % Allowed : 21.28 % Favored : 74.90 % 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 aren not related in a simple way. whole: 2.35 (0.29), residues: 852 helix: 2.80 (0.22), residues: 548 sheet: -0.98 (1.04), residues: 28 loop : -0.83 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 33 TYR 0.037 0.002 TYR H 80 PHE 0.024 0.002 PHE K 39 TRP 0.004 0.001 TRP K 25 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00417 (14186) covalent geometry : angle 0.55620 (20485) hydrogen bonds : bond 0.04743 ( 790) hydrogen bonds : angle 2.83295 ( 1971) metal coordination : bond 0.00860 ( 4) metal coordination : angle 5.29409 ( 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 278 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 250 time to evaluate : 0.240 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: B 88 TYR cc_start: 0.8981 (m-10) cc_final: 0.8685 (m-10) REVERT: D 32 GLU cc_start: 0.8308 (pt0) cc_final: 0.7907 (pt0) REVERT: E 42 ARG cc_start: 0.9032 (mtp180) cc_final: 0.8699 (mtp85) REVERT: F 25 ASN cc_start: 0.8941 (m-40) cc_final: 0.8593 (m-40) REVERT: G 32 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9106 (mm) REVERT: H 102 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8254 (mm-30) REVERT: M 42 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7420 (ttm110) REVERT: M 45 PHE cc_start: 0.8497 (t80) cc_final: 0.7705 (t80) outliers start: 28 outliers final: 25 residues processed: 262 average time/residue: 0.1423 time to fit residues: 50.3887 Evaluate side-chains 270 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 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 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 D residue 119 THR Chi-restraints excluded: chain E residue 48 LEU 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 82 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 71 ASP 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3457 r_free = 0.3457 target = 0.079033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.051002 restraints weight = 38245.124| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.67 r_work: 0.2629 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 14190 Z= 0.374 Angle : 0.695 14.174 20491 Z= 0.397 Chirality : 0.041 0.140 2327 Planarity : 0.005 0.043 1513 Dihedral : 29.617 131.792 4375 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 6.41 % Allowed : 20.46 % Favored : 73.12 % 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 aren not related in a simple way. whole: 1.74 (0.29), residues: 852 helix: 2.31 (0.22), residues: 550 sheet: -1.27 (0.95), residues: 28 loop : -1.04 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 47 TYR 0.052 0.003 TYR H 80 PHE 0.022 0.003 PHE K 32 TRP 0.004 0.001 TRP K 25 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00848 (14186) covalent geometry : angle 0.68604 (20485) hydrogen bonds : bond 0.06742 ( 790) hydrogen bonds : angle 3.53182 ( 1971) metal coordination : bond 0.01285 ( 4) metal coordination : angle 6.57605 ( 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 285 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 0.429 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: 0.9084 (m-10) cc_final: 0.8544 (m-10) REVERT: D 56 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8949 (tpp) REVERT: D 80 TYR cc_start: 0.8567 (m-10) cc_final: 0.8318 (m-80) REVERT: E 42 ARG cc_start: 0.9156 (mtp180) cc_final: 0.8816 (mtp85) REVERT: F 25 ASN cc_start: 0.8985 (m-40) cc_final: 0.8680 (m-40) REVERT: G 32 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9060 (mm) REVERT: G 97 SER cc_start: 0.9600 (p) cc_final: 0.9376 (m) REVERT: K 32 PHE cc_start: 0.7716 (t80) cc_final: 0.7515 (t80) REVERT: M 42 ARG cc_start: 0.7810 (ttm110) cc_final: 0.7126 (ttm110) REVERT: M 43 LEU cc_start: 0.9045 (mm) cc_final: 0.8631 (pt) REVERT: M 45 PHE cc_start: 0.8476 (t80) cc_final: 0.7946 (t80) outliers start: 47 outliers final: 40 residues processed: 262 average time/residue: 0.1393 time to fit residues: 48.4766 Evaluate side-chains 276 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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 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 56 MET 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 74 ILE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 109 LEU 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 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 71 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 86 ILE 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 9 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: 5.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3535 r_free = 0.3535 target = 0.083115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.055338 restraints weight = 37223.166| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.70 r_work: 0.2738 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 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= 0.155 Angle : 0.562 11.306 20491 Z= 0.330 Chirality : 0.033 0.130 2327 Planarity : 0.004 0.033 1513 Dihedral : 29.157 130.606 4375 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.32 % Allowed : 26.19 % 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 aren not related in a simple way. whole: 2.42 (0.29), residues: 852 helix: 2.87 (0.22), residues: 548 sheet: -1.24 (0.94), residues: 28 loop : -0.80 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 33 TYR 0.022 0.002 TYR H 80 PHE 0.017 0.001 PHE K 32 TRP 0.002 0.001 TRP K 25 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00324 (14186) covalent geometry : angle 0.55987 (20485) hydrogen bonds : bond 0.04304 ( 790) hydrogen bonds : angle 2.71475 ( 1971) metal coordination : bond 0.00515 ( 4) metal coordination : angle 3.22188 ( 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 284 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 267 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9414 (mtpp) cc_final: 0.9034 (ttmm) REVERT: C 34 ARG cc_start: 0.8757 (mtm110) cc_final: 0.8418 (ttm-80) REVERT: D 32 GLU cc_start: 0.8431 (pt0) cc_final: 0.8053 (pt0) REVERT: E 42 ARG cc_start: 0.9042 (mtp180) cc_final: 0.8603 (mtp85) REVERT: E 120 MET cc_start: 0.8875 (mtm) cc_final: 0.8303 (mtm) REVERT: F 25 ASN cc_start: 0.8972 (m-40) cc_final: 0.8664 (m-40) REVERT: F 84 MET cc_start: 0.8764 (mmp) cc_final: 0.8532 (mmp) REVERT: G 32 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9090 (mm) REVERT: G 80 ARG cc_start: 0.8417 (tpt170) cc_final: 0.8145 (tpt-90) REVERT: H 76 ARG cc_start: 0.8932 (ttp-110) cc_final: 0.8726 (ttp80) REVERT: M 42 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7198 (ttm110) REVERT: M 43 LEU cc_start: 0.9008 (mm) cc_final: 0.8500 (pt) REVERT: M 45 PHE cc_start: 0.8479 (t80) cc_final: 0.7657 (t80) REVERT: M 70 VAL cc_start: 0.8603 (t) cc_final: 0.8267 (t) outliers start: 17 outliers final: 11 residues processed: 274 average time/residue: 0.1471 time to fit residues: 54.0553 Evaluate side-chains 258 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 246 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 113 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 32 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 0.0030 chunk 6 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.082860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.055044 restraints weight = 37427.900| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.64 r_work: 0.2747 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14190 Z= 0.171 Angle : 0.575 11.493 20491 Z= 0.334 Chirality : 0.033 0.127 2327 Planarity : 0.004 0.045 1513 Dihedral : 29.184 131.646 4375 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.32 % Allowed : 26.06 % Favored : 71.62 % 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 aren not related in a simple way. whole: 2.43 (0.29), residues: 852 helix: 2.90 (0.22), residues: 547 sheet: -1.23 (0.91), residues: 28 loop : -0.84 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 47 TYR 0.023 0.002 TYR D 80 PHE 0.011 0.001 PHE E 67 TRP 0.008 0.002 TRP K 25 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00374 (14186) covalent geometry : angle 0.57299 (20485) hydrogen bonds : bond 0.04451 ( 790) hydrogen bonds : angle 2.79968 ( 1971) metal coordination : bond 0.00699 ( 4) metal coordination : angle 2.68945 ( 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 263 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 246 time to evaluate : 0.294 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 79 LYS cc_start: 0.9410 (mtpp) cc_final: 0.9024 (ttmm) REVERT: B 92 ARG cc_start: 0.9003 (ttp80) cc_final: 0.8771 (tmm-80) REVERT: C 34 ARG cc_start: 0.8732 (mtm110) cc_final: 0.8423 (ttm-80) REVERT: D 117 LYS cc_start: 0.9203 (ttmm) cc_final: 0.8711 (ttpp) REVERT: E 42 ARG cc_start: 0.9094 (mtp180) cc_final: 0.8673 (mtp85) REVERT: E 120 MET cc_start: 0.8920 (mtm) cc_final: 0.8335 (mtm) REVERT: F 25 ASN cc_start: 0.8946 (m-40) cc_final: 0.8653 (m-40) REVERT: G 32 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9153 (mm) REVERT: H 32 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8602 (mt-10) REVERT: M 42 ARG cc_start: 0.7711 (ttm110) cc_final: 0.7047 (ttm110) REVERT: M 43 LEU cc_start: 0.8968 (mm) cc_final: 0.8415 (pt) REVERT: M 45 PHE cc_start: 0.8477 (t80) cc_final: 0.7658 (t80) outliers start: 17 outliers final: 12 residues processed: 255 average time/residue: 0.1300 time to fit residues: 44.8388 Evaluate side-chains 252 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 239 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER 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 F residue 43 VAL 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 M residue 31 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 99 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3537 r_free = 0.3537 target = 0.083158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.055495 restraints weight = 36905.229| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.61 r_work: 0.2749 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14190 Z= 0.179 Angle : 0.581 12.338 20491 Z= 0.337 Chirality : 0.033 0.128 2327 Planarity : 0.004 0.042 1513 Dihedral : 29.156 131.768 4375 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.32 % Allowed : 26.88 % Favored : 70.80 % 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 aren not related in a simple way. whole: 2.28 (0.29), residues: 852 helix: 2.79 (0.22), residues: 556 sheet: -1.33 (0.90), residues: 28 loop : -1.04 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 33 TYR 0.032 0.002 TYR B 88 PHE 0.011 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 covalent geometry : bond 0.00394 (14186) covalent geometry : angle 0.57984 (20485) hydrogen bonds : bond 0.04451 ( 790) hydrogen bonds : angle 2.81082 ( 1971) metal coordination : bond 0.00637 ( 4) metal coordination : angle 2.27933 ( 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 261 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 0.316 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: B 79 LYS cc_start: 0.9416 (mtpp) cc_final: 0.9036 (ttmm) REVERT: B 92 ARG cc_start: 0.8991 (ttp80) cc_final: 0.8780 (tmm-80) REVERT: C 34 ARG cc_start: 0.8723 (mtm110) cc_final: 0.8417 (ttm-80) REVERT: C 92 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8940 (mm) REVERT: E 42 ARG cc_start: 0.9086 (mtp180) cc_final: 0.8673 (mtp85) REVERT: E 73 GLU cc_start: 0.8992 (tp30) cc_final: 0.8764 (tp30) REVERT: E 120 MET cc_start: 0.8919 (mtm) cc_final: 0.8315 (mtm) REVERT: G 32 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9150 (mm) REVERT: H 32 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8588 (mt-10) REVERT: H 76 ARG cc_start: 0.9024 (ttp-110) cc_final: 0.8759 (ttp80) REVERT: M 42 ARG cc_start: 0.7760 (ttm110) cc_final: 0.7094 (ttm110) REVERT: M 43 LEU cc_start: 0.8971 (mm) cc_final: 0.8470 (pt) REVERT: M 45 PHE cc_start: 0.8447 (t80) cc_final: 0.7580 (t80) outliers start: 17 outliers final: 14 residues processed: 253 average time/residue: 0.1257 time to fit residues: 42.9870 Evaluate side-chains 255 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 239 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 43 VAL 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 110 ILE 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: 3.9990 chunk 80 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.080041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.052201 restraints weight = 38028.097| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.67 r_work: 0.2662 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 14190 Z= 0.313 Angle : 0.672 13.941 20491 Z= 0.385 Chirality : 0.039 0.161 2327 Planarity : 0.005 0.050 1513 Dihedral : 29.423 132.936 4375 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.64 % Allowed : 25.24 % Favored : 70.12 % 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 aren not related in a simple way. whole: 1.89 (0.29), residues: 852 helix: 2.43 (0.22), residues: 556 sheet: -1.35 (0.85), residues: 28 loop : -1.08 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 47 TYR 0.040 0.003 TYR D 80 PHE 0.015 0.002 PHE K 32 TRP 0.012 0.003 TRP K 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00710 (14186) covalent geometry : angle 0.67062 (20485) hydrogen bonds : bond 0.05982 ( 790) hydrogen bonds : angle 3.33140 ( 1971) metal coordination : bond 0.01078 ( 4) metal coordination : angle 2.66030 ( 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 263 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.9078 (ttp80) cc_final: 0.8832 (tmm-80) REVERT: D 80 TYR cc_start: 0.8348 (m-10) cc_final: 0.7996 (m-80) REVERT: E 42 ARG cc_start: 0.9151 (mtp180) cc_final: 0.8811 (mtp85) REVERT: F 25 ASN cc_start: 0.9152 (OUTLIER) cc_final: 0.8701 (m-40) REVERT: G 32 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9078 (mm) REVERT: H 56 MET cc_start: 0.8894 (tpp) cc_final: 0.8362 (tpt) REVERT: H 76 ARG cc_start: 0.9111 (ttp-110) cc_final: 0.8844 (ttp80) REVERT: M 42 ARG cc_start: 0.7756 (ttm110) cc_final: 0.7110 (ttm110) REVERT: M 43 LEU cc_start: 0.9021 (mm) cc_final: 0.8517 (pt) REVERT: M 45 PHE cc_start: 0.8517 (t80) cc_final: 0.7707 (t80) outliers start: 34 outliers final: 27 residues processed: 247 average time/residue: 0.1297 time to fit residues: 42.9236 Evaluate side-chains 254 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 47 SER Chi-restraints excluded: chain B residue 60 VAL 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 113 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 43 VAL 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 99 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.082925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.055097 restraints weight = 37055.489| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.66 r_work: 0.2740 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14190 Z= 0.169 Angle : 0.598 12.279 20491 Z= 0.347 Chirality : 0.033 0.142 2327 Planarity : 0.004 0.048 1513 Dihedral : 29.185 131.642 4375 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.46 % Allowed : 26.47 % Favored : 71.08 % 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 aren not related in a simple way. whole: 2.19 (0.29), residues: 852 helix: 2.71 (0.22), residues: 552 sheet: -1.02 (0.92), residues: 28 loop : -1.03 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 47 TYR 0.031 0.002 TYR D 80 PHE 0.014 0.001 PHE E 67 TRP 0.006 0.002 TRP K 25 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00366 (14186) covalent geometry : angle 0.59698 (20485) hydrogen bonds : bond 0.04553 ( 790) hydrogen bonds : angle 2.88179 ( 1971) metal coordination : bond 0.00714 ( 4) metal coordination : angle 2.30386 ( 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 255 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9426 (mtpp) cc_final: 0.9037 (ttmm) REVERT: B 92 ARG cc_start: 0.9021 (ttp80) cc_final: 0.8781 (tmm-80) REVERT: C 34 ARG cc_start: 0.8754 (mtm110) cc_final: 0.8482 (ttm-80) REVERT: E 42 ARG cc_start: 0.9088 (mtp180) cc_final: 0.8678 (mtp85) REVERT: E 73 GLU cc_start: 0.9017 (tp30) cc_final: 0.8726 (tp30) REVERT: E 120 MET cc_start: 0.8899 (mtm) cc_final: 0.8373 (mtm) REVERT: F 25 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8708 (m-40) REVERT: G 32 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9133 (mm) REVERT: G 80 ARG cc_start: 0.8490 (tpt170) cc_final: 0.8206 (tpt-90) REVERT: H 76 ARG cc_start: 0.9066 (ttp-110) cc_final: 0.8762 (ttp80) REVERT: M 42 ARG cc_start: 0.7707 (ttm110) cc_final: 0.7062 (ttm110) REVERT: M 43 LEU cc_start: 0.8997 (mm) cc_final: 0.8493 (pt) REVERT: M 45 PHE cc_start: 0.8497 (t80) cc_final: 0.7666 (t80) outliers start: 18 outliers final: 14 residues processed: 246 average time/residue: 0.1289 time to fit residues: 42.7438 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 : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER 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 98 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 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 Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 HIS ** 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 = 0.3562 r_free = 0.3562 target = 0.084271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.056918 restraints weight = 37421.519| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.67 r_work: 0.2789 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14190 Z= 0.156 Angle : 0.592 12.625 20491 Z= 0.343 Chirality : 0.033 0.169 2327 Planarity : 0.004 0.050 1513 Dihedral : 29.070 130.819 4375 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.18 % Allowed : 27.01 % Favored : 70.80 % 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 aren not related in a simple way. whole: 2.36 (0.29), residues: 852 helix: 2.80 (0.22), residues: 551 sheet: 0.00 (1.23), residues: 18 loop : -0.93 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 47 TYR 0.050 0.002 TYR B 88 PHE 0.013 0.001 PHE E 67 TRP 0.021 0.005 TRP K 25 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00331 (14186) covalent geometry : angle 0.59141 (20485) hydrogen bonds : bond 0.04120 ( 790) hydrogen bonds : angle 2.78664 ( 1971) metal coordination : bond 0.00478 ( 4) metal coordination : angle 2.15436 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3438.92 seconds wall clock time: 59 minutes 13.53 seconds (3553.53 seconds total)