Starting phenix.real_space_refine on Thu Mar 5 03:12:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xzx_33533/03_2026/7xzx_33533.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xzx_33533/03_2026/7xzx_33533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xzx_33533/03_2026/7xzx_33533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xzx_33533/03_2026/7xzx_33533.map" model { file = "/net/cci-nas-00/data/ceres_data/7xzx_33533/03_2026/7xzx_33533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xzx_33533/03_2026/7xzx_33533.cif" } resolution = 4.53 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= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 341 5.49 5 S 78 5.16 5 C 10946 2.51 5 N 3618 2.21 5 O 4287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19270 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3487 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 3507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3507 Classifications: {'DNA': 171} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 170} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1555 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "L" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1555 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "M" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1555 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "N" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1555 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 14, 'TRANS': 183} Time building chain proxies: 4.00, per 1000 atoms: 0.21 Number of scatterers: 19270 At special positions: 0 Unit cell: (170.5, 157.3, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 341 15.00 O 4287 8.00 N 3618 7.00 C 10946 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: 1.33 Conformation dependent library (CDL) restraints added in 516.9 milliseconds 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 18 sheets defined 42.9% alpha, 15.2% beta 166 base pairs and 300 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 44 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 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.292A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.117A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 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 removed outlier: 3.994A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.537A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.553A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.880A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.267A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.523A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 122 Processing helix chain 'K' and resid 165 through 169 Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'K' and resid 277 through 288 Processing helix chain 'K' and resid 289 through 291 No H-bonds generated for 'chain 'K' and resid 289 through 291' Processing helix chain 'L' and resid 165 through 169 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'L' and resid 277 through 288 Processing helix chain 'L' and resid 289 through 291 No H-bonds generated for 'chain 'L' and resid 289 through 291' Processing helix chain 'M' and resid 165 through 169 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'M' and resid 277 through 289 Processing helix chain 'N' and resid 165 through 169 Processing helix chain 'N' and resid 176 through 182 Processing helix chain 'N' and resid 277 through 288 Processing helix chain 'N' and resid 289 through 291 No H-bonds generated for 'chain 'N' and resid 289 through 291' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.999A 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 42 through 43 removed outlier: 7.083A pdb=" N ARG C 42 " --> 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 77 through 78 removed outlier: 3.757A pdb=" N ILE C 78 " --> pdb=" O GLY D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.501A pdb=" N TYR F 98 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.760A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.342A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.547A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 110 through 112 Processing sheet with id=AB3, first strand: chain 'K' and resid 124 through 127 removed outlier: 6.213A pdb=" N LEU K 257 " --> pdb=" O LEU K 265 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG K 267 " --> pdb=" O ILE K 255 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE K 255 " --> pdb=" O ARG K 267 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER K 269 " --> pdb=" O THR K 253 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR K 253 " --> pdb=" O SER K 269 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU K 271 " --> pdb=" O ILE K 251 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE K 251 " --> pdb=" O GLU K 271 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ALA K 161 " --> pdb=" O HIS K 214 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N HIS K 214 " --> pdb=" O ALA K 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 110 through 112 Processing sheet with id=AB5, first strand: chain 'L' and resid 124 through 127 removed outlier: 3.802A pdb=" N ILE L 251 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA L 161 " --> pdb=" O HIS L 214 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N HIS L 214 " --> pdb=" O ALA L 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 110 through 112 Processing sheet with id=AB7, first strand: chain 'M' and resid 124 through 127 removed outlier: 3.832A pdb=" N ILE M 251 " --> pdb=" O VAL M 272 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA M 161 " --> pdb=" O HIS M 214 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS M 214 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 110 through 112 Processing sheet with id=AB9, first strand: chain 'N' and resid 124 through 127 removed outlier: 3.840A pdb=" N ILE N 251 " --> pdb=" O VAL N 272 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ALA N 161 " --> pdb=" O HIS N 214 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N HIS N 214 " --> pdb=" O ALA N 161 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 429 hydrogen bonds 854 hydrogen bond angles 0 basepair planarities 166 basepair parallelities 300 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3653 1.33 - 1.46: 6944 1.46 - 1.59: 8955 1.59 - 1.71: 679 1.71 - 1.84: 112 Bond restraints: 20343 Sorted by residual: bond pdb=" C PRO L 222 " pdb=" O PRO L 222 " ideal model delta sigma weight residual 1.246 1.213 0.033 8.50e-03 1.38e+04 1.48e+01 bond pdb=" C PRO M 222 " pdb=" O PRO M 222 " ideal model delta sigma weight residual 1.240 1.202 0.039 1.12e-02 7.97e+03 1.20e+01 bond pdb=" CA PRO K 190 " pdb=" C PRO K 190 " ideal model delta sigma weight residual 1.514 1.533 -0.019 5.50e-03 3.31e+04 1.15e+01 bond pdb=" N VAL K 122 " pdb=" CA VAL K 122 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N VAL N 225 " pdb=" CA VAL N 225 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.24e-02 6.50e+03 1.06e+01 ... (remaining 20338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 26625 1.73 - 3.47: 2023 3.47 - 5.20: 285 5.20 - 6.93: 22 6.93 - 8.66: 3 Bond angle restraints: 28958 Sorted by residual: angle pdb=" O PRO L 190 " pdb=" C PRO L 190 " pdb=" N PRO L 191 " ideal model delta sigma weight residual 121.31 123.34 -2.03 4.60e-01 4.73e+00 1.96e+01 angle pdb=" N LEU M 265 " pdb=" CA LEU M 265 " pdb=" C LEU M 265 " ideal model delta sigma weight residual 113.88 108.69 5.19 1.23e+00 6.61e-01 1.78e+01 angle pdb=" O PRO K 190 " pdb=" C PRO K 190 " pdb=" N PRO K 191 " ideal model delta sigma weight residual 121.31 123.16 -1.85 4.60e-01 4.73e+00 1.62e+01 angle pdb=" N GLN E 76 " pdb=" CA GLN E 76 " pdb=" CB GLN E 76 " ideal model delta sigma weight residual 110.32 117.14 -6.82 1.70e+00 3.46e-01 1.61e+01 angle pdb=" O PRO M 190 " pdb=" C PRO M 190 " pdb=" N PRO M 191 " ideal model delta sigma weight residual 121.31 123.14 -1.83 4.60e-01 4.73e+00 1.58e+01 ... (remaining 28953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.70: 9312 30.70 - 61.41: 2035 61.41 - 92.11: 63 92.11 - 122.81: 1 122.81 - 153.51: 1 Dihedral angle restraints: 11412 sinusoidal: 6908 harmonic: 4504 Sorted by residual: dihedral pdb=" C4' DC J 33 " pdb=" C3' DC J 33 " pdb=" O3' DC J 33 " pdb=" P DC J 34 " ideal model delta sinusoidal sigma weight residual 220.00 66.49 153.51 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA TYR M 236 " pdb=" C TYR M 236 " pdb=" N MET M 237 " pdb=" CA MET M 237 " ideal model delta harmonic sigma weight residual -180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA TYR K 236 " pdb=" C TYR K 236 " pdb=" N MET K 237 " pdb=" CA MET K 237 " ideal model delta harmonic sigma weight residual 180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 11409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2194 0.051 - 0.102: 774 0.102 - 0.153: 193 0.153 - 0.204: 77 0.204 - 0.256: 9 Chirality restraints: 3247 Sorted by residual: chirality pdb=" CA ARG L 248 " pdb=" N ARG L 248 " pdb=" C ARG L 248 " pdb=" CB ARG L 248 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ARG N 248 " pdb=" N ARG N 248 " pdb=" C ARG N 248 " pdb=" CB ARG N 248 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA GLU C 61 " pdb=" N GLU C 61 " pdb=" C GLU C 61 " pdb=" CB GLU C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 3244 not shown) Planarity restraints: 2533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 52 " 0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C ALA G 52 " -0.077 2.00e-02 2.50e+03 pdb=" O ALA G 52 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA G 53 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C LYS F 59 " -0.053 2.00e-02 2.50e+03 pdb=" O LYS F 59 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL F 60 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 32 " 0.038 2.00e-02 2.50e+03 1.74e-02 7.61e+00 pdb=" N1 DT I 32 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DT I 32 " -0.010 2.00e-02 2.50e+03 pdb=" O2 DT I 32 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DT I 32 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DT I 32 " 0.006 2.00e-02 2.50e+03 pdb=" O4 DT I 32 " 0.024 2.00e-02 2.50e+03 pdb=" C5 DT I 32 " -0.010 2.00e-02 2.50e+03 pdb=" C7 DT I 32 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DT I 32 " -0.021 2.00e-02 2.50e+03 ... (remaining 2530 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 39 2.33 - 2.97: 8793 2.97 - 3.61: 30401 3.61 - 4.26: 51634 4.26 - 4.90: 76401 Nonbonded interactions: 167268 Sorted by model distance: nonbonded pdb=" NZ LYS C 75 " pdb=" P DA J 157 " model vdw 1.688 3.480 nonbonded pdb=" CD1 LEU G 23 " pdb=" OE1 GLU G 56 " model vdw 1.717 3.460 nonbonded pdb=" NZ LYS C 75 " pdb=" OP1 DA J 157 " model vdw 1.752 3.120 nonbonded pdb=" NH2 ARG G 17 " pdb=" OP2 DA J 55 " model vdw 1.851 3.120 nonbonded pdb=" NH2 ARG F 36 " pdb=" OP1 DA J 85 " model vdw 1.906 3.120 ... (remaining 167263 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 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.940 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: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.890 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3738 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 20343 Z= 0.351 Angle : 0.987 8.665 28958 Z= 0.645 Chirality : 0.060 0.256 3247 Planarity : 0.005 0.045 2533 Dihedral : 25.641 153.511 8512 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.15 % Allowed : 2.82 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 1530 helix: 0.79 (0.18), residues: 629 sheet: 0.45 (0.26), residues: 312 loop : 0.31 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 267 TYR 0.026 0.003 TYR B 88 PHE 0.018 0.002 PHE N 270 TRP 0.005 0.002 TRP N 146 HIS 0.010 0.002 HIS K 233 Details of bonding type rmsd covalent geometry : bond 0.00609 (20343) covalent geometry : angle 0.98724 (28958) hydrogen bonds : bond 0.11687 ( 1059) hydrogen bonds : angle 5.43389 ( 2621) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8908 (mp0) cc_final: 0.8642 (mp0) REVERT: B 61 PHE cc_start: 0.8162 (t80) cc_final: 0.7950 (t80) REVERT: B 63 GLU cc_start: 0.8532 (pt0) cc_final: 0.8078 (pp20) REVERT: D 66 ILE cc_start: 0.9287 (mm) cc_final: 0.8980 (mm) REVERT: E 105 GLU cc_start: 0.8592 (tp30) cc_final: 0.8107 (tm-30) REVERT: G 25 PHE cc_start: 0.8614 (m-80) cc_final: 0.8034 (m-80) REVERT: G 54 VAL cc_start: 0.9539 (m) cc_final: 0.9224 (m) REVERT: K 243 MET cc_start: 0.3388 (ptp) cc_final: 0.2774 (ptt) REVERT: L 160 MET cc_start: 0.3291 (ttm) cc_final: 0.2313 (mtp) outliers start: 2 outliers final: 0 residues processed: 266 average time/residue: 0.1483 time to fit residues: 58.8176 Evaluate side-chains 141 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 overall best weight: 4.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN F 75 HIS G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 ASN L 239 ASN L 288 ASN M 104 GLN M 178 HIS M 193 HIS M 235 ASN M 239 ASN M 268 ASN M 288 ASN N 214 HIS N 268 ASN N 288 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.091029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.064711 restraints weight = 200998.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.064604 restraints weight = 113684.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.065358 restraints weight = 74604.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.065563 restraints weight = 54299.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.066409 restraints weight = 45378.521| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 20343 Z= 0.231 Angle : 0.698 8.280 28958 Z= 0.399 Chirality : 0.042 0.240 3247 Planarity : 0.006 0.043 2533 Dihedral : 29.317 157.486 5455 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.30 % Allowed : 2.75 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.20), residues: 1530 helix: 1.44 (0.19), residues: 627 sheet: 0.84 (0.27), residues: 300 loop : 0.51 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 175 TYR 0.022 0.002 TYR F 88 PHE 0.026 0.003 PHE E 104 TRP 0.021 0.003 TRP N 146 HIS 0.007 0.001 HIS N 233 Details of bonding type rmsd covalent geometry : bond 0.00521 (20343) covalent geometry : angle 0.69763 (28958) hydrogen bonds : bond 0.06775 ( 1059) hydrogen bonds : angle 4.09543 ( 2621) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 0.556 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 73 GLU cc_start: 0.8252 (tp30) cc_final: 0.7910 (tp30) REVERT: A 84 PHE cc_start: 0.8969 (m-10) cc_final: 0.8623 (m-10) REVERT: A 105 GLU cc_start: 0.9164 (tp30) cc_final: 0.8895 (tp30) REVERT: A 106 ASP cc_start: 0.8836 (m-30) cc_final: 0.8621 (m-30) REVERT: B 53 GLU cc_start: 0.9145 (mp0) cc_final: 0.8835 (mp0) REVERT: B 63 GLU cc_start: 0.8865 (pt0) cc_final: 0.8237 (pp20) REVERT: B 81 VAL cc_start: 0.8311 (m) cc_final: 0.8030 (m) REVERT: D 59 MET cc_start: 0.9151 (mmp) cc_final: 0.8894 (mmm) REVERT: D 65 ASP cc_start: 0.9264 (t0) cc_final: 0.9035 (t0) REVERT: E 105 GLU cc_start: 0.9164 (tp30) cc_final: 0.8485 (tm-30) REVERT: E 119 ILE cc_start: 0.8449 (pt) cc_final: 0.8152 (pt) REVERT: G 25 PHE cc_start: 0.8935 (m-10) cc_final: 0.8649 (m-10) REVERT: G 38 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7165 (t0) REVERT: H 51 ILE cc_start: 0.7993 (tt) cc_final: 0.6935 (mp) REVERT: K 162 ILE cc_start: 0.3605 (pt) cc_final: 0.3322 (mp) REVERT: L 205 TYR cc_start: -0.2472 (m-80) cc_final: -0.2923 (m-10) outliers start: 4 outliers final: 1 residues processed: 188 average time/residue: 0.1323 time to fit residues: 38.9934 Evaluate side-chains 124 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 140 optimal weight: 30.0000 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 121 optimal weight: 50.0000 chunk 134 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 147 optimal weight: 40.0000 chunk 167 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS C 24 GLN H 46 HIS K 239 ASN M 100 GLN N 193 HIS N 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.072183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.043144 restraints weight = 175243.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.043284 restraints weight = 104193.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.043743 restraints weight = 72836.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.043964 restraints weight = 57266.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.044289 restraints weight = 49749.356| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 20343 Z= 0.276 Angle : 0.760 15.925 28958 Z= 0.431 Chirality : 0.044 0.245 3247 Planarity : 0.006 0.048 2533 Dihedral : 29.736 162.666 5455 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.37 % Allowed : 4.01 % Favored : 95.62 % 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 are not related in a simple way. whole: 0.84 (0.20), residues: 1530 helix: 1.05 (0.19), residues: 627 sheet: 0.37 (0.27), residues: 324 loop : 0.32 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG L 196 TYR 0.043 0.004 TYR D 37 PHE 0.034 0.003 PHE N 212 TRP 0.007 0.001 TRP L 146 HIS 0.015 0.002 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00608 (20343) covalent geometry : angle 0.75997 (28958) hydrogen bonds : bond 0.07148 ( 1059) hydrogen bonds : angle 4.49232 ( 2621) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 147 time to evaluate : 0.605 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 73 GLU cc_start: 0.8550 (tp30) cc_final: 0.7939 (tp30) REVERT: A 84 PHE cc_start: 0.9196 (m-10) cc_final: 0.8756 (m-10) REVERT: A 105 GLU cc_start: 0.9047 (tp30) cc_final: 0.8681 (tm-30) REVERT: A 106 ASP cc_start: 0.9087 (m-30) cc_final: 0.8213 (m-30) REVERT: A 120 MET cc_start: 0.7572 (mmp) cc_final: 0.6953 (mmm) REVERT: B 50 ILE cc_start: 0.9140 (mm) cc_final: 0.8873 (mm) REVERT: B 53 GLU cc_start: 0.9277 (mp0) cc_final: 0.8963 (mp0) REVERT: B 63 GLU cc_start: 0.9073 (pt0) cc_final: 0.8538 (pp20) REVERT: E 105 GLU cc_start: 0.9297 (tp30) cc_final: 0.8968 (tm-30) REVERT: F 50 ILE cc_start: 0.8956 (mm) cc_final: 0.8699 (mm) REVERT: F 84 MET cc_start: 0.9076 (tpp) cc_final: 0.8659 (tpp) REVERT: G 65 LEU cc_start: 0.9641 (tp) cc_final: 0.9433 (tp) REVERT: H 32 GLU cc_start: 0.8179 (tp30) cc_final: 0.7925 (mp0) REVERT: H 65 ASP cc_start: 0.9502 (t70) cc_final: 0.9289 (t0) REVERT: K 162 ILE cc_start: 0.3970 (pt) cc_final: 0.3545 (mp) REVERT: K 246 MET cc_start: 0.5868 (mtm) cc_final: 0.5606 (mtt) outliers start: 5 outliers final: 1 residues processed: 149 average time/residue: 0.1227 time to fit residues: 28.9157 Evaluate side-chains 105 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 151 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 139 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** L 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 GLN N 233 HIS N 235 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.069031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.039279 restraints weight = 172944.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.039240 restraints weight = 101223.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.039629 restraints weight = 71406.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.039971 restraints weight = 56636.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.040178 restraints weight = 48948.658| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.7039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 20343 Z= 0.208 Angle : 0.634 10.586 28958 Z= 0.364 Chirality : 0.040 0.249 3247 Planarity : 0.005 0.066 2533 Dihedral : 29.650 165.033 5455 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.07 % Allowed : 2.23 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.21), residues: 1530 helix: 1.44 (0.20), residues: 629 sheet: 0.55 (0.27), residues: 328 loop : 0.24 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 39 TYR 0.030 0.002 TYR H 80 PHE 0.019 0.002 PHE K 109 TRP 0.017 0.002 TRP N 146 HIS 0.009 0.001 HIS L 178 Details of bonding type rmsd covalent geometry : bond 0.00451 (20343) covalent geometry : angle 0.63446 (28958) hydrogen bonds : bond 0.05573 ( 1059) hydrogen bonds : angle 4.04744 ( 2621) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.392 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 73 GLU cc_start: 0.8851 (tp30) cc_final: 0.8282 (tp30) REVERT: A 84 PHE cc_start: 0.9187 (m-10) cc_final: 0.8647 (m-10) REVERT: A 105 GLU cc_start: 0.9289 (tp30) cc_final: 0.8956 (tm-30) REVERT: A 106 ASP cc_start: 0.9178 (m-30) cc_final: 0.8268 (m-30) REVERT: B 50 ILE cc_start: 0.9274 (mm) cc_final: 0.8942 (mm) REVERT: B 53 GLU cc_start: 0.9331 (mp0) cc_final: 0.8994 (mp0) REVERT: B 63 GLU cc_start: 0.9123 (pt0) cc_final: 0.8639 (pp20) REVERT: B 68 ASP cc_start: 0.9045 (m-30) cc_final: 0.8845 (m-30) REVERT: D 59 MET cc_start: 0.9678 (mmp) cc_final: 0.9468 (mmm) REVERT: D 65 ASP cc_start: 0.9350 (t0) cc_final: 0.9107 (t0) REVERT: E 77 ASP cc_start: 0.9161 (m-30) cc_final: 0.8657 (m-30) REVERT: E 106 ASP cc_start: 0.9161 (m-30) cc_final: 0.8453 (p0) REVERT: F 50 ILE cc_start: 0.9024 (mm) cc_final: 0.8492 (mm) REVERT: F 53 GLU cc_start: 0.9506 (mp0) cc_final: 0.9234 (pm20) REVERT: G 65 LEU cc_start: 0.9625 (tp) cc_final: 0.9358 (tp) REVERT: H 65 ASP cc_start: 0.9488 (t70) cc_final: 0.9281 (t0) REVERT: K 246 MET cc_start: 0.5204 (mtm) cc_final: 0.4960 (mtt) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.1373 time to fit residues: 30.2607 Evaluate side-chains 98 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 131 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 159 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 100 GLN ** K 165 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 = 0.3737 r_free = 0.3737 target = 0.075135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.044894 restraints weight = 205147.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.045422 restraints weight = 108065.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 91)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.045493 restraints weight = 72467.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.045741 restraints weight = 56075.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.045704 restraints weight = 46163.708| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.7511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20343 Z= 0.171 Angle : 0.573 8.334 28958 Z= 0.332 Chirality : 0.037 0.165 3247 Planarity : 0.004 0.062 2533 Dihedral : 29.602 166.251 5455 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.21), residues: 1530 helix: 1.78 (0.20), residues: 630 sheet: 0.66 (0.28), residues: 328 loop : 0.23 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 40 TYR 0.023 0.002 TYR L 205 PHE 0.012 0.001 PHE F 61 TRP 0.006 0.001 TRP L 146 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00374 (20343) covalent geometry : angle 0.57321 (28958) hydrogen bonds : bond 0.05118 ( 1059) hydrogen bonds : angle 3.91744 ( 2621) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8830 (tp30) cc_final: 0.8197 (tp30) REVERT: A 84 PHE cc_start: 0.9024 (m-10) cc_final: 0.8687 (m-10) REVERT: A 105 GLU cc_start: 0.9367 (tp30) cc_final: 0.8967 (tm-30) REVERT: B 50 ILE cc_start: 0.9314 (mm) cc_final: 0.8970 (mm) REVERT: B 53 GLU cc_start: 0.9410 (mp0) cc_final: 0.9106 (mp0) REVERT: B 63 GLU cc_start: 0.9198 (pt0) cc_final: 0.8685 (pp20) REVERT: B 68 ASP cc_start: 0.9110 (m-30) cc_final: 0.8898 (m-30) REVERT: D 59 MET cc_start: 0.9703 (mmp) cc_final: 0.9490 (mmm) REVERT: E 77 ASP cc_start: 0.9423 (m-30) cc_final: 0.9153 (m-30) REVERT: E 90 MET cc_start: 0.9611 (mmp) cc_final: 0.9370 (mmm) REVERT: E 110 CYS cc_start: 0.9569 (t) cc_final: 0.9277 (p) REVERT: F 50 ILE cc_start: 0.8862 (mm) cc_final: 0.8488 (mm) REVERT: F 53 GLU cc_start: 0.9505 (mp0) cc_final: 0.9286 (pm20) REVERT: F 79 LYS cc_start: 0.8995 (mppt) cc_final: 0.8792 (mmtm) REVERT: F 84 MET cc_start: 0.8361 (tpp) cc_final: 0.8116 (tpp) REVERT: H 56 MET cc_start: 0.9548 (mmp) cc_final: 0.9098 (mmm) REVERT: K 202 ARG cc_start: 0.5771 (tmt170) cc_final: 0.5570 (tpt90) REVERT: L 205 TYR cc_start: -0.1247 (m-10) cc_final: -0.1743 (m-10) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1342 time to fit residues: 26.6841 Evaluate side-chains 93 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 93 optimal weight: 10.0000 chunk 179 optimal weight: 50.0000 chunk 168 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 180 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 HIS L 193 HIS ** M 193 HIS ** 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 = 0.3690 r_free = 0.3690 target = 0.073061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.042923 restraints weight = 207507.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.042477 restraints weight = 113674.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.043102 restraints weight = 77037.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.043179 restraints weight = 59624.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.043211 restraints weight = 50591.535| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.8334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 20343 Z= 0.191 Angle : 0.590 10.582 28958 Z= 0.339 Chirality : 0.038 0.201 3247 Planarity : 0.004 0.035 2533 Dihedral : 29.430 170.352 5455 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.21), residues: 1530 helix: 1.75 (0.20), residues: 630 sheet: 0.84 (0.29), residues: 316 loop : 0.17 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 32 TYR 0.022 0.002 TYR L 205 PHE 0.021 0.001 PHE E 67 TRP 0.008 0.001 TRP L 146 HIS 0.031 0.002 HIS M 193 Details of bonding type rmsd covalent geometry : bond 0.00423 (20343) covalent geometry : angle 0.59013 (28958) hydrogen bonds : bond 0.05549 ( 1059) hydrogen bonds : angle 3.90596 ( 2621) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8836 (tp30) cc_final: 0.8165 (tp30) REVERT: A 84 PHE cc_start: 0.9135 (m-10) cc_final: 0.8795 (m-10) REVERT: A 105 GLU cc_start: 0.9408 (tp30) cc_final: 0.9072 (tm-30) REVERT: A 120 MET cc_start: 0.7833 (mmm) cc_final: 0.7317 (mmm) REVERT: B 50 ILE cc_start: 0.9292 (mm) cc_final: 0.8974 (mm) REVERT: B 53 GLU cc_start: 0.9436 (mp0) cc_final: 0.9194 (mp0) REVERT: B 63 GLU cc_start: 0.9278 (pt0) cc_final: 0.8737 (pp20) REVERT: E 77 ASP cc_start: 0.9484 (m-30) cc_final: 0.9229 (m-30) REVERT: E 90 MET cc_start: 0.9563 (mmp) cc_final: 0.9257 (mmm) REVERT: E 106 ASP cc_start: 0.8394 (m-30) cc_final: 0.8123 (p0) REVERT: E 110 CYS cc_start: 0.9583 (t) cc_final: 0.9272 (p) REVERT: F 50 ILE cc_start: 0.8845 (mm) cc_final: 0.8455 (mm) REVERT: F 53 GLU cc_start: 0.9544 (mp0) cc_final: 0.9238 (pm20) REVERT: F 79 LYS cc_start: 0.9049 (mppt) cc_final: 0.8777 (mmtm) REVERT: G 91 GLU cc_start: 0.9140 (pm20) cc_final: 0.8931 (pm20) REVERT: K 246 MET cc_start: 0.4657 (mtm) cc_final: 0.4009 (ptp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1439 time to fit residues: 24.6505 Evaluate side-chains 81 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 161 optimal weight: 50.0000 chunk 8 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 169 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 115 optimal weight: 40.0000 chunk 12 optimal weight: 9.9990 chunk 162 optimal weight: 40.0000 chunk 53 optimal weight: 20.0000 chunk 167 optimal weight: 40.0000 overall best weight: 11.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN F 75 HIS G 24 GLN L 235 ASN M 104 GLN ** M 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.061097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.030714 restraints weight = 186201.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.031105 restraints weight = 112046.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.031361 restraints weight = 84188.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.031489 restraints weight = 67763.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.031585 restraints weight = 59980.076| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 1.0026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 20343 Z= 0.369 Angle : 0.788 16.184 28958 Z= 0.443 Chirality : 0.045 0.280 3247 Planarity : 0.006 0.073 2533 Dihedral : 29.781 174.433 5455 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1530 helix: 0.77 (0.20), residues: 631 sheet: 0.67 (0.30), residues: 288 loop : -0.00 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG K 290 TYR 0.055 0.003 TYR H 80 PHE 0.015 0.002 PHE E 67 TRP 0.008 0.001 TRP K 146 HIS 0.011 0.002 HIS N 178 Details of bonding type rmsd covalent geometry : bond 0.00806 (20343) covalent geometry : angle 0.78752 (28958) hydrogen bonds : bond 0.10245 ( 1059) hydrogen bonds : angle 4.89850 ( 2621) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.430 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 105 GLU cc_start: 0.9332 (tp30) cc_final: 0.9113 (tm-30) REVERT: A 120 MET cc_start: 0.8587 (mmm) cc_final: 0.8214 (mmm) REVERT: B 63 GLU cc_start: 0.9363 (pt0) cc_final: 0.8913 (pp20) REVERT: E 90 MET cc_start: 0.9626 (mmp) cc_final: 0.9299 (mmm) REVERT: K 202 ARG cc_start: 0.5420 (tmt170) cc_final: 0.5217 (tpt90) REVERT: K 246 MET cc_start: 0.5370 (mtm) cc_final: 0.4767 (mtm) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1341 time to fit residues: 19.1793 Evaluate side-chains 72 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 122 optimal weight: 30.0000 chunk 157 optimal weight: 40.0000 chunk 132 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 139 optimal weight: 50.0000 chunk 89 optimal weight: 30.0000 chunk 168 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 125 optimal weight: 40.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 214 HIS M 104 GLN ** M 168 HIS ** 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 = 0.3542 r_free = 0.3542 target = 0.062167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.031139 restraints weight = 181437.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.031473 restraints weight = 107067.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.031621 restraints weight = 76140.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.031871 restraints weight = 60588.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.031902 restraints weight = 55127.644| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 1.0291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 20343 Z= 0.210 Angle : 0.628 17.034 28958 Z= 0.356 Chirality : 0.039 0.197 3247 Planarity : 0.004 0.053 2533 Dihedral : 29.878 177.694 5455 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.21), residues: 1530 helix: 1.24 (0.20), residues: 630 sheet: 0.56 (0.29), residues: 316 loop : -0.05 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 290 TYR 0.029 0.002 TYR H 80 PHE 0.010 0.001 PHE E 67 TRP 0.005 0.001 TRP K 146 HIS 0.007 0.001 HIS N 233 Details of bonding type rmsd covalent geometry : bond 0.00458 (20343) covalent geometry : angle 0.62807 (28958) hydrogen bonds : bond 0.05968 ( 1059) hydrogen bonds : angle 4.21098 ( 2621) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.9209 (m-10) cc_final: 0.8545 (m-10) REVERT: A 120 MET cc_start: 0.8289 (mmm) cc_final: 0.7824 (mmm) REVERT: B 63 GLU cc_start: 0.9349 (pt0) cc_final: 0.8833 (pp20) REVERT: B 85 ASP cc_start: 0.9176 (m-30) cc_final: 0.8462 (t70) REVERT: E 90 MET cc_start: 0.9563 (mmp) cc_final: 0.9224 (mmm) REVERT: F 50 ILE cc_start: 0.8796 (mm) cc_final: 0.8520 (mm) REVERT: F 63 GLU cc_start: 0.9389 (mt-10) cc_final: 0.8946 (mt-10) REVERT: F 68 ASP cc_start: 0.9283 (m-30) cc_final: 0.9079 (m-30) REVERT: K 246 MET cc_start: 0.5295 (mtm) cc_final: 0.4718 (mtm) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1252 time to fit residues: 18.8826 Evaluate side-chains 67 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 1 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 110 optimal weight: 0.0970 chunk 163 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 88 optimal weight: 40.0000 overall best weight: 6.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 168 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 = 0.3520 r_free = 0.3520 target = 0.061177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.030777 restraints weight = 182330.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.030383 restraints weight = 108321.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.030527 restraints weight = 77786.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.030755 restraints weight = 63946.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.030833 restraints weight = 57138.257| |-----------------------------------------------------------------------------| r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 1.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20343 Z= 0.241 Angle : 0.646 13.425 28958 Z= 0.368 Chirality : 0.039 0.192 3247 Planarity : 0.005 0.044 2533 Dihedral : 29.634 178.759 5455 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.21), residues: 1530 helix: 1.25 (0.20), residues: 626 sheet: 0.62 (0.30), residues: 288 loop : -0.29 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 72 TYR 0.030 0.002 TYR H 80 PHE 0.010 0.002 PHE E 67 TRP 0.005 0.001 TRP K 146 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00522 (20343) covalent geometry : angle 0.64608 (28958) hydrogen bonds : bond 0.06891 ( 1059) hydrogen bonds : angle 4.29786 ( 2621) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7988 (m-10) cc_final: 0.7643 (m-80) REVERT: A 84 PHE cc_start: 0.9161 (m-10) cc_final: 0.8641 (m-80) REVERT: A 120 MET cc_start: 0.8358 (mmm) cc_final: 0.7873 (mmm) REVERT: B 63 GLU cc_start: 0.9376 (pt0) cc_final: 0.8882 (pp20) REVERT: B 85 ASP cc_start: 0.9201 (m-30) cc_final: 0.8479 (t70) REVERT: E 90 MET cc_start: 0.9541 (mmp) cc_final: 0.9175 (mmm) REVERT: E 105 GLU cc_start: 0.9191 (pp20) cc_final: 0.8361 (pp20) REVERT: F 50 ILE cc_start: 0.8837 (mm) cc_final: 0.8514 (mm) REVERT: F 63 GLU cc_start: 0.9404 (mt-10) cc_final: 0.8953 (mt-10) REVERT: F 68 ASP cc_start: 0.9282 (m-30) cc_final: 0.9070 (m-30) REVERT: F 74 GLU cc_start: 0.8870 (tp30) cc_final: 0.8599 (tm-30) REVERT: K 246 MET cc_start: 0.5346 (mtm) cc_final: 0.4785 (mtm) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1300 time to fit residues: 19.2866 Evaluate side-chains 68 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 137 optimal weight: 0.0270 chunk 20 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 106 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 136 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 overall best weight: 6.2050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** M 168 HIS ** 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 = 0.3516 r_free = 0.3516 target = 0.061296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.030665 restraints weight = 183873.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030297 restraints weight = 108145.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.030446 restraints weight = 76995.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.030681 restraints weight = 60168.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.030927 restraints weight = 54530.590| |-----------------------------------------------------------------------------| r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 1.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20343 Z= 0.208 Angle : 0.622 13.629 28958 Z= 0.354 Chirality : 0.039 0.172 3247 Planarity : 0.004 0.035 2533 Dihedral : 29.658 177.418 5455 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.21), residues: 1530 helix: 1.42 (0.20), residues: 626 sheet: 0.60 (0.32), residues: 264 loop : -0.41 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 273 TYR 0.027 0.002 TYR H 80 PHE 0.013 0.001 PHE E 104 TRP 0.005 0.001 TRP L 146 HIS 0.007 0.001 HIS N 233 Details of bonding type rmsd covalent geometry : bond 0.00449 (20343) covalent geometry : angle 0.62217 (28958) hydrogen bonds : bond 0.05406 ( 1059) hydrogen bonds : angle 4.24083 ( 2621) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.606 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 84 PHE cc_start: 0.9080 (m-10) cc_final: 0.8577 (m-80) REVERT: A 105 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8449 (tm-30) REVERT: A 120 MET cc_start: 0.8357 (mmm) cc_final: 0.7860 (mmm) REVERT: B 63 GLU cc_start: 0.9387 (pt0) cc_final: 0.8901 (pp20) REVERT: B 85 ASP cc_start: 0.9228 (m-30) cc_final: 0.8487 (t70) REVERT: E 90 MET cc_start: 0.9549 (mmp) cc_final: 0.9171 (mmm) REVERT: E 106 ASP cc_start: 0.8820 (m-30) cc_final: 0.8602 (p0) REVERT: F 50 ILE cc_start: 0.8691 (mm) cc_final: 0.8226 (mm) REVERT: F 63 GLU cc_start: 0.9415 (mt-10) cc_final: 0.8967 (mt-10) REVERT: F 68 ASP cc_start: 0.9280 (m-30) cc_final: 0.9070 (m-30) REVERT: F 74 GLU cc_start: 0.8864 (tp30) cc_final: 0.8605 (tm-30) REVERT: K 246 MET cc_start: 0.5366 (mtm) cc_final: 0.4790 (mtm) REVERT: N 237 MET cc_start: 0.5805 (tpp) cc_final: 0.5426 (mmp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1198 time to fit residues: 18.0564 Evaluate side-chains 69 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 123 optimal weight: 40.0000 chunk 97 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 0.0370 chunk 86 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 167 optimal weight: 0.0870 chunk 151 optimal weight: 30.0000 overall best weight: 1.4040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN H 60 ASN ** M 168 HIS ** 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 = 0.3545 r_free = 0.3545 target = 0.062508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.030908 restraints weight = 178132.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.031420 restraints weight = 103434.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.031569 restraints weight = 72473.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.031743 restraints weight = 57101.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.031806 restraints weight = 50627.965| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 1.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20343 Z= 0.140 Angle : 0.574 10.363 28958 Z= 0.327 Chirality : 0.037 0.163 3247 Planarity : 0.004 0.039 2533 Dihedral : 29.386 179.949 5455 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.21), residues: 1530 helix: 1.75 (0.21), residues: 626 sheet: 0.51 (0.31), residues: 292 loop : -0.35 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 273 TYR 0.025 0.001 TYR H 80 PHE 0.013 0.001 PHE M 113 TRP 0.003 0.000 TRP K 146 HIS 0.007 0.001 HIS N 233 Details of bonding type rmsd covalent geometry : bond 0.00294 (20343) covalent geometry : angle 0.57422 (28958) hydrogen bonds : bond 0.04510 ( 1059) hydrogen bonds : angle 3.82609 ( 2621) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5382.99 seconds wall clock time: 93 minutes 9.16 seconds (5589.16 seconds total)