Starting phenix.real_space_refine on Wed Jul 30 23:10:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pp6_17796/07_2025/8pp6_17796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pp6_17796/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8pp6_17796/07_2025/8pp6_17796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pp6_17796/07_2025/8pp6_17796.map" model { file = "/net/cci-nas-00/data/ceres_data/8pp6_17796/07_2025/8pp6_17796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pp6_17796/07_2025/8pp6_17796.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.74, per 1000 atoms: 0.66 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: 3.71 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 7.05 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: 5.23 Time building geometry restraints manager: 4.44 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 42.060 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.910 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.010 0.002 TRP K 25 HIS 0.003 0.001 HIS E 39 PHE 0.015 0.002 PHE K 39 TYR 0.012 0.002 TYR B 72 ARG 0.008 0.001 ARG G 70 Details of bonding type rmsd hydrogen bonds : bond 0.13402 ( 790) hydrogen bonds : angle 3.74001 ( 1971) metal coordination : bond 0.00683 ( 4) metal coordination : angle 7.86947 ( 6) covalent geometry : bond 0.00454 (14186) covalent geometry : angle 0.56294 (20485) *********************** 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 : 1.025 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: 0.3440 time to fit residues: 143.1604 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 : 1.020 ------------------------------------------------------------------------------- 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 94 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.0870 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.081557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.053173 restraints weight = 36768.004| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.68 r_work: 0.2680 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14190 Z= 0.257 Angle : 0.638 16.057 20491 Z= 0.363 Chirality : 0.037 0.127 2327 Planarity : 0.005 0.031 1513 Dihedral : 29.518 132.997 4377 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.37 % Allowed : 17.05 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.29), residues: 852 helix: 2.49 (0.22), residues: 549 sheet: -0.66 (1.33), residues: 17 loop : -1.02 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP K 25 HIS 0.004 0.001 HIS B 75 PHE 0.013 0.002 PHE E 67 TYR 0.026 0.002 TYR H 80 ARG 0.009 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.06014 ( 790) hydrogen bonds : angle 3.18598 ( 1971) metal coordination : bond 0.01192 ( 4) metal coordination : angle 10.77156 ( 6) covalent geometry : bond 0.00582 (14186) covalent geometry : angle 0.61132 (20485) *********************** 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 299 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 267 time to evaluate : 0.962 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: 0.8619 (mmp80) cc_final: 0.8036 (mmm-85) REVERT: B 88 TYR cc_start: 0.8915 (m-10) cc_final: 0.8673 (m-10) REVERT: D 32 GLU cc_start: 0.8443 (pt0) cc_final: 0.8169 (pt0) REVERT: E 120 MET cc_start: 0.8914 (mtm) cc_final: 0.8269 (mtm) REVERT: M 45 PHE cc_start: 0.8382 (t80) cc_final: 0.7882 (t80) outliers start: 32 outliers final: 20 residues processed: 278 average time/residue: 0.3426 time to fit residues: 127.6075 Evaluate side-chains 262 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain H residue 117 LYS 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 1 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.082297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.054110 restraints weight = 37160.127| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.65 r_work: 0.2703 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14190 Z= 0.194 Angle : 0.578 12.184 20491 Z= 0.336 Chirality : 0.034 0.126 2327 Planarity : 0.004 0.035 1513 Dihedral : 29.352 131.344 4375 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.23 % Allowed : 19.51 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.29), residues: 852 helix: 2.64 (0.22), residues: 549 sheet: -1.07 (1.01), residues: 28 loop : -0.96 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 25 HIS 0.003 0.001 HIS B 75 PHE 0.016 0.002 PHE K 39 TYR 0.033 0.002 TYR H 80 ARG 0.007 0.001 ARG K 33 Details of bonding type rmsd hydrogen bonds : bond 0.04987 ( 790) hydrogen bonds : angle 2.92657 ( 1971) metal coordination : bond 0.01056 ( 4) metal coordination : angle 7.16724 ( 6) covalent geometry : bond 0.00428 (14186) covalent geometry : angle 0.56483 (20485) *********************** 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 : 1.075 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: 0.8563 (mmp80) cc_final: 0.8015 (mmm-85) REVERT: B 88 TYR cc_start: 0.8970 (m-10) cc_final: 0.8649 (m-10) REVERT: D 32 GLU cc_start: 0.8300 (pt0) cc_final: 0.7945 (pt0) REVERT: E 42 ARG cc_start: 0.9030 (mtp180) cc_final: 0.8692 (mtp85) REVERT: E 59 GLU cc_start: 0.8146 (pm20) cc_final: 0.7803 (pm20) REVERT: E 94 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8507 (tt0) REVERT: E 120 MET cc_start: 0.8904 (mtm) cc_final: 0.8290 (mtm) REVERT: G 70 ARG cc_start: 0.9052 (tpp80) cc_final: 0.8786 (ttp-170) REVERT: K 40 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7458 (tptm) REVERT: K 47 ARG cc_start: 0.8238 (mtm-85) cc_final: 0.7744 (mpp80) REVERT: M 44 ILE cc_start: 0.8805 (mm) cc_final: 0.8518 (tp) REVERT: M 45 PHE cc_start: 0.8506 (t80) cc_final: 0.8288 (t80) outliers start: 31 outliers final: 25 residues processed: 262 average time/residue: 0.3167 time to fit residues: 110.6973 Evaluate side-chains 261 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 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 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 119 THR Chi-restraints excluded: chain M residue 42 ARG Chi-restraints excluded: chain M residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.082333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.054232 restraints weight = 37041.595| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.65 r_work: 0.2711 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14190 Z= 0.194 Angle : 0.566 11.267 20491 Z= 0.332 Chirality : 0.034 0.126 2327 Planarity : 0.004 0.035 1513 Dihedral : 29.266 131.144 4375 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.23 % Allowed : 21.96 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.29), residues: 852 helix: 2.78 (0.22), residues: 551 sheet: -0.97 (1.05), residues: 28 loop : -0.95 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 25 HIS 0.004 0.001 HIS F 75 PHE 0.015 0.002 PHE K 32 TYR 0.037 0.002 TYR H 80 ARG 0.007 0.001 ARG K 33 Details of bonding type rmsd hydrogen bonds : bond 0.04831 ( 790) hydrogen bonds : angle 2.84726 ( 1971) metal coordination : bond 0.00836 ( 4) metal coordination : angle 4.79284 ( 6) covalent geometry : bond 0.00428 (14186) covalent geometry : angle 0.56031 (20485) *********************** 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 279 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8975 (m-10) cc_final: 0.8653 (m-10) REVERT: C 34 ARG cc_start: 0.8778 (mtm110) cc_final: 0.8434 (ttm-80) REVERT: D 32 GLU cc_start: 0.8257 (pt0) cc_final: 0.7848 (pt0) REVERT: D 98 LEU cc_start: 0.8914 (mm) cc_final: 0.8692 (mm) REVERT: E 42 ARG cc_start: 0.9044 (mtp180) cc_final: 0.8705 (mtp85) REVERT: E 94 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8451 (tt0) REVERT: E 120 MET cc_start: 0.8900 (mtm) cc_final: 0.8284 (mtm) REVERT: F 25 ASN cc_start: 0.8973 (m-40) cc_final: 0.8630 (m-40) REVERT: G 32 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9064 (mm) REVERT: G 70 ARG cc_start: 0.9039 (tpp80) cc_final: 0.8746 (ttp-170) REVERT: H 102 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8465 (mm-30) REVERT: K 47 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.7535 (mpp80) REVERT: M 45 PHE cc_start: 0.8414 (t80) cc_final: 0.7653 (t80) outliers start: 31 outliers final: 25 residues processed: 260 average time/residue: 0.3167 time to fit residues: 110.6958 Evaluate side-chains 261 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 46 VAL 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 H residue 108 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 35 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.0050 chunk 26 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.082818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.054774 restraints weight = 37436.537| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.65 r_work: 0.2730 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14190 Z= 0.177 Angle : 0.556 11.006 20491 Z= 0.327 Chirality : 0.033 0.126 2327 Planarity : 0.004 0.035 1513 Dihedral : 29.196 131.573 4375 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.96 % Allowed : 22.51 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.29), residues: 852 helix: 2.81 (0.22), residues: 554 sheet: -0.91 (1.05), residues: 28 loop : -0.93 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 25 HIS 0.003 0.001 HIS F 75 PHE 0.023 0.002 PHE K 32 TYR 0.028 0.002 TYR H 80 ARG 0.004 0.000 ARG C 70 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 790) hydrogen bonds : angle 2.76307 ( 1971) metal coordination : bond 0.00650 ( 4) metal coordination : angle 4.03070 ( 6) covalent geometry : bond 0.00387 (14186) covalent geometry : angle 0.55193 (20485) *********************** 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 277 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 248 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ARG cc_start: 0.8770 (mtm110) cc_final: 0.8432 (ttm-80) REVERT: D 80 TYR cc_start: 0.8212 (m-10) cc_final: 0.7997 (m-80) REVERT: D 98 LEU cc_start: 0.8867 (mm) cc_final: 0.8498 (mm) REVERT: D 117 LYS cc_start: 0.9246 (ttmm) cc_final: 0.8624 (ttpp) REVERT: E 42 ARG cc_start: 0.9065 (mtp180) cc_final: 0.8628 (mtp85) REVERT: G 32 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9089 (mm) REVERT: G 70 ARG cc_start: 0.8911 (tpp80) cc_final: 0.8532 (ttp-170) REVERT: H 102 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8353 (mm-30) REVERT: K 47 ARG cc_start: 0.8240 (mtm-85) cc_final: 0.7487 (mpp80) REVERT: M 43 LEU cc_start: 0.9005 (mm) cc_final: 0.8577 (pt) REVERT: M 45 PHE cc_start: 0.8552 (t80) cc_final: 0.7695 (t80) outliers start: 29 outliers final: 24 residues processed: 261 average time/residue: 0.3155 time to fit residues: 110.6752 Evaluate side-chains 258 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 60 VAL 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 51 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 119 THR 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 110 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain M residue 42 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 70 optimal weight: 0.3980 chunk 11 optimal weight: 0.0470 chunk 40 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.085136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.057662 restraints weight = 37374.482| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.70 r_work: 0.2797 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3313 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= 0.143 Angle : 0.543 10.161 20491 Z= 0.319 Chirality : 0.032 0.128 2327 Planarity : 0.004 0.032 1513 Dihedral : 29.048 131.491 4375 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.59 % Allowed : 24.01 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.29), residues: 852 helix: 3.02 (0.22), residues: 553 sheet: -0.90 (1.01), residues: 28 loop : -0.81 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP K 25 HIS 0.004 0.001 HIS E 113 PHE 0.017 0.001 PHE K 32 TYR 0.020 0.002 TYR H 80 ARG 0.007 0.000 ARG K 33 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 790) hydrogen bonds : angle 2.54442 ( 1971) metal coordination : bond 0.00358 ( 4) metal coordination : angle 2.84707 ( 6) covalent geometry : bond 0.00299 (14186) covalent geometry : angle 0.54113 (20485) *********************** 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 278 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 259 time to evaluate : 1.069 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: 0.8757 (mtm110) cc_final: 0.8455 (ttm-80) REVERT: D 98 LEU cc_start: 0.8874 (mm) cc_final: 0.8647 (mm) REVERT: E 42 ARG cc_start: 0.9033 (mtp180) cc_final: 0.8705 (mtp85) REVERT: F 25 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8658 (m-40) REVERT: G 32 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9089 (mm) REVERT: G 70 ARG cc_start: 0.8809 (tpp80) cc_final: 0.8399 (ttp-170) REVERT: M 43 LEU cc_start: 0.8998 (mm) cc_final: 0.8544 (pt) REVERT: M 45 PHE cc_start: 0.8524 (t80) cc_final: 0.7678 (t80) outliers start: 19 outliers final: 11 residues processed: 267 average time/residue: 0.3110 time to fit residues: 112.2722 Evaluate side-chains 260 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 247 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 25 ASN 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 Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 42 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 11 optimal weight: 0.0870 overall best weight: 3.1764 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.081894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.054120 restraints weight = 37278.262| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.69 r_work: 0.2699 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14190 Z= 0.242 Angle : 0.603 11.781 20491 Z= 0.349 Chirality : 0.036 0.284 2327 Planarity : 0.004 0.036 1513 Dihedral : 29.211 132.743 4375 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.96 % Allowed : 22.37 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.29), residues: 852 helix: 2.82 (0.22), residues: 554 sheet: -1.18 (0.99), residues: 28 loop : -0.82 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP K 25 HIS 0.004 0.001 HIS B 75 PHE 0.015 0.002 PHE K 32 TYR 0.036 0.002 TYR H 80 ARG 0.005 0.000 ARG F 23 Details of bonding type rmsd hydrogen bonds : bond 0.05052 ( 790) hydrogen bonds : angle 2.92452 ( 1971) metal coordination : bond 0.00771 ( 4) metal coordination : angle 3.44702 ( 6) covalent geometry : bond 0.00546 (14186) covalent geometry : angle 0.60067 (20485) *********************** 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 268 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8896 (m-10) cc_final: 0.8509 (m-10) REVERT: B 92 ARG cc_start: 0.9050 (ttp80) cc_final: 0.8837 (tmm-80) REVERT: C 34 ARG cc_start: 0.8745 (mtm110) cc_final: 0.8374 (ttm-80) REVERT: D 98 LEU cc_start: 0.8912 (mm) cc_final: 0.8647 (mm) REVERT: E 42 ARG cc_start: 0.9056 (mtp180) cc_final: 0.8632 (mtp85) REVERT: F 25 ASN cc_start: 0.9175 (m-40) cc_final: 0.8722 (m-40) REVERT: G 32 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9053 (mm) REVERT: G 70 ARG cc_start: 0.8796 (tpp80) cc_final: 0.8420 (ttp-170) REVERT: H 40 LYS cc_start: 0.9336 (mtmt) cc_final: 0.9134 (ttmm) REVERT: K 47 ARG cc_start: 0.8272 (mtm-85) cc_final: 0.7649 (mpp80) REVERT: K 48 LYS cc_start: 0.8551 (tttp) cc_final: 0.8175 (tttm) REVERT: M 43 LEU cc_start: 0.9005 (mm) cc_final: 0.8558 (pt) REVERT: M 45 PHE cc_start: 0.8521 (t80) cc_final: 0.7701 (t80) outliers start: 29 outliers final: 21 residues processed: 253 average time/residue: 0.3142 time to fit residues: 106.9044 Evaluate side-chains 254 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 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 D residue 119 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 42 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 111 optimal weight: 30.0000 chunk 29 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 G 37 ASN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.081963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.054262 restraints weight = 37695.201| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.64 r_work: 0.2719 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3397 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= 0.210 Angle : 0.599 12.251 20491 Z= 0.347 Chirality : 0.035 0.228 2327 Planarity : 0.004 0.037 1513 Dihedral : 29.205 132.422 4375 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.37 % Allowed : 22.37 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.29), residues: 852 helix: 2.67 (0.22), residues: 560 sheet: -1.30 (0.97), residues: 28 loop : -1.02 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K 25 HIS 0.003 0.001 HIS E 113 PHE 0.017 0.002 PHE K 32 TYR 0.021 0.002 TYR C 56 ARG 0.003 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.04834 ( 790) hydrogen bonds : angle 2.89274 ( 1971) metal coordination : bond 0.00736 ( 4) metal coordination : angle 2.96600 ( 6) covalent geometry : bond 0.00471 (14186) covalent geometry : angle 0.59707 (20485) *********************** 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 267 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8977 (m-10) cc_final: 0.8633 (m-10) REVERT: B 92 ARG cc_start: 0.9024 (ttp80) cc_final: 0.8818 (tmm-80) REVERT: C 34 ARG cc_start: 0.8771 (mtm110) cc_final: 0.8418 (ttm-80) REVERT: D 98 LEU cc_start: 0.8952 (mm) cc_final: 0.8688 (mm) REVERT: E 42 ARG cc_start: 0.9075 (mtp180) cc_final: 0.8661 (mtp85) REVERT: F 25 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8668 (m-40) REVERT: G 32 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9071 (mm) REVERT: G 70 ARG cc_start: 0.8811 (tpp80) cc_final: 0.8469 (ttp-170) REVERT: H 40 LYS cc_start: 0.9347 (mtmt) cc_final: 0.9132 (ttmm) REVERT: K 47 ARG cc_start: 0.8320 (mtm-85) cc_final: 0.7569 (mpp80) REVERT: K 48 LYS cc_start: 0.8584 (tttp) cc_final: 0.8241 (tttm) REVERT: M 43 LEU cc_start: 0.9002 (mm) cc_final: 0.8459 (pt) REVERT: M 45 PHE cc_start: 0.8545 (t80) cc_final: 0.7672 (t80) outliers start: 32 outliers final: 26 residues processed: 250 average time/residue: 0.3186 time to fit residues: 106.6962 Evaluate side-chains 257 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 113 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 60 LEU 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 50 ILE 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 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 Chi-restraints excluded: chain M residue 42 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 37 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.084241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.056881 restraints weight = 36950.631| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.65 r_work: 0.2774 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14190 Z= 0.151 Angle : 0.573 12.315 20491 Z= 0.334 Chirality : 0.033 0.249 2327 Planarity : 0.004 0.043 1513 Dihedral : 29.065 131.805 4375 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.46 % Allowed : 23.74 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.29), residues: 852 helix: 2.86 (0.22), residues: 556 sheet: -1.24 (0.96), residues: 28 loop : -0.90 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K 25 HIS 0.004 0.001 HIS E 113 PHE 0.015 0.001 PHE K 32 TYR 0.020 0.002 TYR C 56 ARG 0.006 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 790) hydrogen bonds : angle 2.63656 ( 1971) metal coordination : bond 0.00450 ( 4) metal coordination : angle 2.25756 ( 6) covalent geometry : bond 0.00321 (14186) covalent geometry : angle 0.57131 (20485) *********************** 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 265 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.9004 (m-40) cc_final: 0.8585 (m-40) REVERT: B 79 LYS cc_start: 0.9395 (mtpp) cc_final: 0.8966 (ttmm) REVERT: B 88 TYR cc_start: 0.8870 (m-10) cc_final: 0.8430 (m-10) REVERT: C 34 ARG cc_start: 0.8744 (mtm110) cc_final: 0.8459 (ttm-80) REVERT: D 98 LEU cc_start: 0.8922 (mm) cc_final: 0.8652 (mm) REVERT: E 42 ARG cc_start: 0.9058 (mtp180) cc_final: 0.8635 (mtp85) REVERT: E 73 GLU cc_start: 0.8999 (tp30) cc_final: 0.8685 (tp30) REVERT: F 25 ASN cc_start: 0.9162 (m110) cc_final: 0.8696 (m-40) REVERT: G 32 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9080 (mm) REVERT: G 70 ARG cc_start: 0.8781 (tpp80) cc_final: 0.8402 (ttp-170) REVERT: H 76 ARG cc_start: 0.9013 (ttp-110) cc_final: 0.8780 (ttp80) REVERT: K 47 ARG cc_start: 0.8263 (mtm-85) cc_final: 0.7646 (mpp80) REVERT: M 43 LEU cc_start: 0.8974 (mm) cc_final: 0.8452 (pt) REVERT: M 45 PHE cc_start: 0.8527 (t80) cc_final: 0.7642 (t80) outliers start: 18 outliers final: 15 residues processed: 257 average time/residue: 0.2991 time to fit residues: 103.6014 Evaluate side-chains 256 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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 97 LEU 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 Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain M residue 42 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 62 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 37 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 = 0.082526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.054973 restraints weight = 37276.273| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.62 r_work: 0.2741 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14190 Z= 0.199 Angle : 0.600 11.894 20491 Z= 0.346 Chirality : 0.034 0.179 2327 Planarity : 0.004 0.042 1513 Dihedral : 29.137 132.172 4375 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.86 % Allowed : 24.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.29), residues: 852 helix: 2.70 (0.22), residues: 561 sheet: -1.14 (0.95), residues: 28 loop : -1.00 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.005 TRP K 25 HIS 0.003 0.001 HIS B 75 PHE 0.013 0.001 PHE K 32 TYR 0.019 0.002 TYR C 56 ARG 0.005 0.000 ARG K 33 Details of bonding type rmsd hydrogen bonds : bond 0.04663 ( 790) hydrogen bonds : angle 2.82281 ( 1971) metal coordination : bond 0.00671 ( 4) metal coordination : angle 2.68630 ( 6) covalent geometry : bond 0.00443 (14186) covalent geometry : angle 0.59796 (20485) ********************** 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 256 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 235 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8732 (tmm-80) cc_final: 0.8429 (tpt-90) REVERT: C 34 ARG cc_start: 0.8772 (mtm110) cc_final: 0.8409 (ttm-80) REVERT: D 56 MET cc_start: 0.9158 (tpt) cc_final: 0.8924 (tpp) REVERT: D 98 LEU cc_start: 0.8937 (mm) cc_final: 0.8569 (mm) REVERT: E 42 ARG cc_start: 0.9090 (mtp180) cc_final: 0.8671 (mtp85) REVERT: E 73 GLU cc_start: 0.9011 (tp30) cc_final: 0.8716 (tp30) REVERT: F 25 ASN cc_start: 0.9086 (m110) cc_final: 0.8692 (m-40) REVERT: G 32 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9075 (mm) REVERT: G 70 ARG cc_start: 0.8768 (tpp80) cc_final: 0.8401 (ttp-170) REVERT: H 40 LYS cc_start: 0.9340 (mtmt) cc_final: 0.9139 (ttmm) REVERT: H 76 ARG cc_start: 0.9008 (ttp-110) cc_final: 0.8753 (ttp80) REVERT: K 47 ARG cc_start: 0.8300 (mtm-85) cc_final: 0.7732 (mpp80) REVERT: M 43 LEU cc_start: 0.8999 (mm) cc_final: 0.8445 (pt) REVERT: M 45 PHE cc_start: 0.8537 (t80) cc_final: 0.7659 (t80) outliers start: 21 outliers final: 16 residues processed: 245 average time/residue: 0.3197 time to fit residues: 104.4911 Evaluate side-chains 250 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 78 ILE 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 119 THR Chi-restraints excluded: chain E residue 46 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 H residue 84 SER Chi-restraints excluded: chain M residue 42 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.0030 chunk 16 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.2394 ------------------------------------------------------------------------------- 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 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.083788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.056506 restraints weight = 37263.420| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.67 r_work: 0.2782 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3716 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= 0.160 Angle : 0.578 11.796 20491 Z= 0.335 Chirality : 0.033 0.176 2327 Planarity : 0.004 0.046 1513 Dihedral : 29.034 131.567 4375 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.59 % Allowed : 24.42 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.29), residues: 852 helix: 2.74 (0.22), residues: 561 sheet: -0.95 (0.96), residues: 28 loop : -0.94 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP K 25 HIS 0.004 0.001 HIS E 113 PHE 0.013 0.001 PHE E 67 TYR 0.027 0.002 TYR D 80 ARG 0.006 0.000 ARG K 33 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 790) hydrogen bonds : angle 2.70035 ( 1971) metal coordination : bond 0.00513 ( 4) metal coordination : angle 2.55072 ( 6) covalent geometry : bond 0.00347 (14186) covalent geometry : angle 0.57634 (20485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8074.20 seconds wall clock time: 138 minutes 39.86 seconds (8319.86 seconds total)