Starting phenix.real_space_refine on Mon Jun 16 13:11:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xzx_33533/06_2025/7xzx_33533.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xzx_33533/06_2025/7xzx_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_33533/06_2025/7xzx_33533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xzx_33533/06_2025/7xzx_33533.map" model { file = "/net/cci-nas-00/data/ceres_data/7xzx_33533/06_2025/7xzx_33533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xzx_33533/06_2025/7xzx_33533.cif" } resolution = 4.53 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= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.75, per 1000 atoms: 0.61 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: 5.13 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 8.33 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: 7.27 Time building geometry restraints manager: 6.09 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 50.200 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.410 ------------------------------------------------------------------------------- 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 (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: 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 TRP 0.005 0.002 TRP N 146 HIS 0.010 0.002 HIS K 233 PHE 0.018 0.002 PHE N 270 TYR 0.026 0.003 TYR B 88 ARG 0.008 0.001 ARG M 267 Details of bonding type rmsd hydrogen bonds : bond 0.11687 ( 1059) hydrogen bonds : angle 5.43389 ( 2621) covalent geometry : bond 0.00609 (20343) covalent geometry : angle 0.98724 (28958) *********************** 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 : 1.829 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: 0.8163 (t80) cc_final: 0.7950 (t80) REVERT: B 63 GLU cc_start: 0.8533 (pt0) cc_final: 0.8078 (pp20) REVERT: D 66 ILE cc_start: 0.9288 (mm) cc_final: 0.8981 (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: 0.2773 (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: 0.3516 time to fit residues: 137.7121 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 : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.4980 chunk 137 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 142 optimal weight: 50.0000 chunk 55 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 106 optimal weight: 50.0000 chunk 165 optimal weight: 3.9990 overall best weight: 5.2992 ------------------------------------------------------------------------------- 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 ** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.088423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.061635 restraints weight = 200881.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.061539 restraints weight = 114183.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.062176 restraints weight = 74359.316| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 20343 Z= 0.263 Angle : 0.762 11.228 28958 Z= 0.430 Chirality : 0.044 0.230 3247 Planarity : 0.007 0.059 2533 Dihedral : 29.335 158.861 5455 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.30 % Allowed : 3.12 % Favored : 96.59 % 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: 1.05 (0.20), residues: 1530 helix: 1.13 (0.19), residues: 621 sheet: 0.74 (0.27), residues: 300 loop : 0.40 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP N 146 HIS 0.009 0.002 HIS F 75 PHE 0.031 0.003 PHE E 104 TYR 0.025 0.002 TYR L 205 ARG 0.014 0.001 ARG N 175 Details of bonding type rmsd hydrogen bonds : bond 0.08216 ( 1059) hydrogen bonds : angle 4.28245 ( 2621) covalent geometry : bond 0.00585 (20343) covalent geometry : angle 0.76174 (28958) *********************** 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 179 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 175 time to evaluate : 1.663 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: A 51 ILE cc_start: 0.8332 (mt) cc_final: 0.8123 (pt) REVERT: A 73 GLU cc_start: 0.8573 (tp30) cc_final: 0.8067 (tp30) REVERT: A 84 PHE cc_start: 0.9081 (m-10) cc_final: 0.8735 (m-10) REVERT: A 105 GLU cc_start: 0.9218 (tp30) cc_final: 0.8928 (tp30) REVERT: A 106 ASP cc_start: 0.8909 (m-30) cc_final: 0.8696 (m-30) REVERT: B 53 GLU cc_start: 0.9213 (mp0) cc_final: 0.8923 (mp0) REVERT: B 63 GLU cc_start: 0.8877 (pt0) cc_final: 0.8346 (pp20) REVERT: B 93 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8515 (tm-30) REVERT: D 49 THR cc_start: 0.7037 (m) cc_final: 0.6688 (m) REVERT: D 59 MET cc_start: 0.9182 (mmp) cc_final: 0.8971 (mmm) REVERT: D 65 ASP cc_start: 0.9299 (t0) cc_final: 0.9062 (t0) REVERT: E 64 LYS cc_start: 0.8266 (pttm) cc_final: 0.8054 (ptpp) REVERT: E 105 GLU cc_start: 0.9236 (tp30) cc_final: 0.8637 (tm-30) REVERT: K 162 ILE cc_start: 0.3444 (pt) cc_final: 0.3041 (mp) REVERT: K 243 MET cc_start: 0.2160 (ptp) cc_final: 0.1919 (ptt) REVERT: L 205 TYR cc_start: -0.2438 (m-80) cc_final: -0.2898 (m-10) outliers start: 4 outliers final: 1 residues processed: 179 average time/residue: 0.3233 time to fit residues: 90.1802 Evaluate side-chains 120 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 137 optimal weight: 40.0000 chunk 83 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 112 GLN E 68 GLN H 46 HIS K 200 ASN K 239 ASN N 100 GLN N 193 HIS N 239 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.074016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.045230 restraints weight = 171710.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.045459 restraints weight = 103045.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.045882 restraints weight = 72340.241| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20343 Z= 0.226 Angle : 0.712 16.639 28958 Z= 0.405 Chirality : 0.043 0.278 3247 Planarity : 0.006 0.102 2533 Dihedral : 29.841 162.555 5455 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.30 % Allowed : 2.60 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.18 (0.20), residues: 1530 helix: 1.53 (0.19), residues: 626 sheet: 0.43 (0.27), residues: 320 loop : 0.33 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 146 HIS 0.010 0.002 HIS E 113 PHE 0.022 0.002 PHE K 134 TYR 0.029 0.002 TYR K 220 ARG 0.025 0.001 ARG L 196 Details of bonding type rmsd hydrogen bonds : bond 0.05669 ( 1059) hydrogen bonds : angle 4.18419 ( 2621) covalent geometry : bond 0.00478 (20343) covalent geometry : angle 0.71238 (28958) *********************** 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 154 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8558 (tp30) cc_final: 0.7979 (tp30) REVERT: A 84 PHE cc_start: 0.9028 (m-10) cc_final: 0.8503 (m-10) REVERT: A 105 GLU cc_start: 0.9128 (tp30) cc_final: 0.8775 (tm-30) REVERT: A 106 ASP cc_start: 0.9127 (m-30) cc_final: 0.8227 (m-30) REVERT: B 53 GLU cc_start: 0.9261 (mp0) cc_final: 0.8985 (mp0) REVERT: B 63 GLU cc_start: 0.9129 (pt0) cc_final: 0.8594 (pp20) REVERT: D 59 MET cc_start: 0.9449 (mmp) cc_final: 0.9100 (mmm) REVERT: E 94 GLU cc_start: 0.9413 (mm-30) cc_final: 0.9210 (mm-30) REVERT: E 105 GLU cc_start: 0.9262 (tp30) cc_final: 0.8961 (tm-30) REVERT: F 50 ILE cc_start: 0.8877 (mm) cc_final: 0.8609 (mm) REVERT: F 63 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8899 (mt-10) REVERT: G 65 LEU cc_start: 0.9598 (tp) cc_final: 0.9376 (tp) REVERT: H 34 TYR cc_start: 0.9240 (m-10) cc_final: 0.8989 (m-10) REVERT: K 133 MET cc_start: 0.5239 (ppp) cc_final: 0.4717 (ppp) REVERT: K 246 MET cc_start: 0.5204 (mtm) cc_final: 0.4998 (mtt) outliers start: 4 outliers final: 1 residues processed: 154 average time/residue: 0.2961 time to fit residues: 72.4276 Evaluate side-chains 108 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 54 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 118 optimal weight: 40.0000 chunk 15 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 154 optimal weight: 30.0000 chunk 109 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 233 HIS N 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.068649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.038721 restraints weight = 172570.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.039216 restraints weight = 102285.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.039434 restraints weight = 72382.558| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.6941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 20343 Z= 0.245 Angle : 0.658 10.291 28958 Z= 0.377 Chirality : 0.040 0.229 3247 Planarity : 0.005 0.076 2533 Dihedral : 29.463 165.211 5455 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.07 % Allowed : 2.45 % Favored : 97.48 % 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: 1.29 (0.20), residues: 1530 helix: 1.51 (0.20), residues: 627 sheet: 0.95 (0.31), residues: 260 loop : 0.28 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 146 HIS 0.006 0.001 HIS M 178 PHE 0.017 0.002 PHE K 109 TYR 0.027 0.002 TYR C 39 ARG 0.017 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.07547 ( 1059) hydrogen bonds : angle 4.19054 ( 2621) covalent geometry : bond 0.00541 (20343) covalent geometry : angle 0.65763 (28958) *********************** 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 128 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 2.204 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: 0.8897 (tp30) cc_final: 0.8291 (tp30) REVERT: A 84 PHE cc_start: 0.9083 (m-10) cc_final: 0.8633 (m-10) REVERT: A 105 GLU cc_start: 0.9249 (tp30) cc_final: 0.8896 (tm-30) REVERT: A 106 ASP cc_start: 0.9183 (m-30) cc_final: 0.8301 (m-30) REVERT: B 50 ILE cc_start: 0.9209 (mm) cc_final: 0.8558 (mm) REVERT: B 53 GLU cc_start: 0.9392 (mp0) cc_final: 0.8909 (pm20) REVERT: B 63 GLU cc_start: 0.9130 (pt0) cc_final: 0.8653 (pp20) REVERT: D 65 ASP cc_start: 0.9352 (t0) cc_final: 0.9114 (t0) REVERT: E 77 ASP cc_start: 0.9196 (m-30) cc_final: 0.8941 (m-30) REVERT: E 106 ASP cc_start: 0.9125 (m-30) cc_final: 0.8448 (p0) REVERT: E 110 CYS cc_start: 0.9490 (t) cc_final: 0.9279 (p) REVERT: F 50 ILE cc_start: 0.8890 (mm) cc_final: 0.8418 (mm) REVERT: F 53 GLU cc_start: 0.9551 (mp0) cc_final: 0.9254 (pm20) REVERT: F 84 MET cc_start: 0.8629 (tpp) cc_final: 0.8226 (tpt) REVERT: G 56 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8811 (mm-30) REVERT: G 65 LEU cc_start: 0.9636 (tp) cc_final: 0.9387 (tp) REVERT: H 34 TYR cc_start: 0.9392 (m-10) cc_final: 0.9188 (m-10) REVERT: K 246 MET cc_start: 0.5006 (mtm) cc_final: 0.4785 (mtt) REVERT: L 169 MET cc_start: 0.3953 (tpt) cc_final: 0.3736 (tpt) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.3179 time to fit residues: 65.3821 Evaluate side-chains 92 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 58 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 179 optimal weight: 30.0000 chunk 71 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 154 optimal weight: 50.0000 chunk 170 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 144 optimal weight: 50.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 HIS ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 HIS N 233 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.074758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.045407 restraints weight = 207864.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.045046 restraints weight = 112407.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.045205 restraints weight = 75394.876| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.7523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20343 Z= 0.188 Angle : 0.586 10.022 28958 Z= 0.340 Chirality : 0.038 0.173 3247 Planarity : 0.005 0.090 2533 Dihedral : 29.649 167.227 5455 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: 1.51 (0.21), residues: 1530 helix: 1.86 (0.20), residues: 623 sheet: 0.84 (0.29), residues: 312 loop : 0.27 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 146 HIS 0.014 0.001 HIS M 193 PHE 0.012 0.001 PHE E 67 TYR 0.020 0.002 TYR L 205 ARG 0.015 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.05136 ( 1059) hydrogen bonds : angle 3.95804 ( 2621) covalent geometry : bond 0.00411 (20343) covalent geometry : angle 0.58645 (28958) *********************** 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 121 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.8962 (m-10) cc_final: 0.8625 (m-10) REVERT: A 105 GLU cc_start: 0.9377 (tp30) cc_final: 0.8964 (tm-30) REVERT: B 50 ILE cc_start: 0.9280 (mm) cc_final: 0.8954 (mm) REVERT: B 53 GLU cc_start: 0.9416 (mp0) cc_final: 0.9128 (mp0) REVERT: B 63 GLU cc_start: 0.9204 (pt0) cc_final: 0.8715 (pp20) REVERT: B 68 ASP cc_start: 0.9133 (m-30) cc_final: 0.8928 (m-30) REVERT: D 59 MET cc_start: 0.9713 (mmp) cc_final: 0.9507 (mmm) REVERT: E 90 MET cc_start: 0.9510 (mmp) cc_final: 0.9296 (mmm) REVERT: E 110 CYS cc_start: 0.9576 (t) cc_final: 0.9268 (p) REVERT: F 50 ILE cc_start: 0.8776 (mm) cc_final: 0.8460 (mm) REVERT: F 53 GLU cc_start: 0.9534 (mp0) cc_final: 0.9241 (pm20) REVERT: F 63 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8823 (mp0) REVERT: G 56 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8636 (mm-30) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2884 time to fit residues: 55.6474 Evaluate side-chains 88 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 124 optimal weight: 0.0770 chunk 116 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 168 optimal weight: 0.1980 chunk 16 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 179 optimal weight: 50.0000 chunk 154 optimal weight: 40.0000 chunk 172 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 233 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.075946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.045890 restraints weight = 205071.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.045253 restraints weight = 111098.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.045847 restraints weight = 73662.349| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.7621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20343 Z= 0.136 Angle : 0.549 7.933 28958 Z= 0.315 Chirality : 0.037 0.176 3247 Planarity : 0.004 0.060 2533 Dihedral : 29.429 168.748 5455 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 1.62 (0.21), residues: 1530 helix: 1.97 (0.20), residues: 624 sheet: 1.00 (0.30), residues: 292 loop : 0.27 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 146 HIS 0.014 0.001 HIS K 178 PHE 0.022 0.001 PHE K 134 TYR 0.042 0.001 TYR H 80 ARG 0.025 0.000 ARG K 290 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 1059) hydrogen bonds : angle 3.64861 ( 2621) covalent geometry : bond 0.00282 (20343) covalent geometry : angle 0.54919 (28958) *********************** 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 126 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.623 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: 0.8783 (tp30) cc_final: 0.8171 (tp30) REVERT: A 84 PHE cc_start: 0.8854 (m-10) cc_final: 0.8389 (m-10) REVERT: A 105 GLU cc_start: 0.9412 (tp30) cc_final: 0.8979 (tm-30) REVERT: B 50 ILE cc_start: 0.9313 (mm) cc_final: 0.8967 (mm) REVERT: B 53 GLU cc_start: 0.9436 (mp0) cc_final: 0.9135 (mp0) REVERT: B 63 GLU cc_start: 0.9215 (pt0) cc_final: 0.8696 (pp20) REVERT: B 68 ASP cc_start: 0.9119 (m-30) cc_final: 0.8888 (m-30) REVERT: C 56 GLU cc_start: 0.9282 (pp20) cc_final: 0.8955 (mt-10) REVERT: D 59 MET cc_start: 0.9626 (mmp) cc_final: 0.9370 (mmm) REVERT: D 65 ASP cc_start: 0.9420 (t0) cc_final: 0.9124 (t0) REVERT: E 77 ASP cc_start: 0.9270 (m-30) cc_final: 0.8652 (m-30) REVERT: E 90 MET cc_start: 0.9504 (mmp) cc_final: 0.9239 (mmm) REVERT: E 97 GLU cc_start: 0.8983 (pp20) cc_final: 0.8656 (pp20) REVERT: E 106 ASP cc_start: 0.8972 (m-30) cc_final: 0.8500 (p0) REVERT: E 110 CYS cc_start: 0.9615 (t) cc_final: 0.9264 (p) REVERT: F 50 ILE cc_start: 0.8762 (mm) cc_final: 0.8350 (mm) REVERT: F 53 GLU cc_start: 0.9525 (mp0) cc_final: 0.9197 (pm20) REVERT: F 68 ASP cc_start: 0.9277 (m-30) cc_final: 0.8868 (m-30) REVERT: G 56 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8759 (mm-30) REVERT: H 34 TYR cc_start: 0.9408 (m-80) cc_final: 0.9195 (m-80) REVERT: L 237 MET cc_start: 0.7135 (ptp) cc_final: 0.6915 (ptt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2977 time to fit residues: 59.3079 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 : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 46 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 169 optimal weight: 50.0000 chunk 84 optimal weight: 10.0000 chunk 7 optimal weight: 0.2980 chunk 41 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- 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** N 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.074670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.045650 restraints weight = 206777.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.044204 restraints weight = 121486.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.044744 restraints weight = 74307.717| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.8007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20343 Z= 0.147 Angle : 0.541 7.928 28958 Z= 0.313 Chirality : 0.036 0.161 3247 Planarity : 0.004 0.035 2533 Dihedral : 29.185 169.720 5455 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: 1.69 (0.21), residues: 1530 helix: 2.18 (0.20), residues: 624 sheet: 0.81 (0.29), residues: 308 loop : 0.24 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 146 HIS 0.003 0.001 HIS K 193 PHE 0.032 0.001 PHE E 104 TYR 0.027 0.001 TYR H 80 ARG 0.019 0.000 ARG K 196 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 1059) hydrogen bonds : angle 3.61704 ( 2621) covalent geometry : bond 0.00315 (20343) covalent geometry : angle 0.54062 (28958) *********************** 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 120 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 2.566 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: 0.8806 (tp30) cc_final: 0.8219 (tp30) REVERT: A 84 PHE cc_start: 0.8812 (m-10) cc_final: 0.8411 (m-10) REVERT: A 105 GLU cc_start: 0.9365 (tp30) cc_final: 0.8989 (tm-30) REVERT: B 50 ILE cc_start: 0.9239 (mm) cc_final: 0.8906 (mm) REVERT: B 53 GLU cc_start: 0.9439 (mp0) cc_final: 0.9174 (mp0) REVERT: B 63 GLU cc_start: 0.9241 (pt0) cc_final: 0.8722 (pp20) REVERT: B 68 ASP cc_start: 0.9163 (m-30) cc_final: 0.8944 (m-30) REVERT: D 59 MET cc_start: 0.9615 (mmp) cc_final: 0.9336 (mmm) REVERT: D 65 ASP cc_start: 0.9421 (t0) cc_final: 0.9168 (t0) REVERT: E 90 MET cc_start: 0.9460 (mmp) cc_final: 0.9213 (mmm) REVERT: E 106 ASP cc_start: 0.8892 (m-30) cc_final: 0.8415 (p0) REVERT: E 110 CYS cc_start: 0.9554 (t) cc_final: 0.9233 (p) REVERT: F 50 ILE cc_start: 0.8719 (mm) cc_final: 0.8295 (mm) REVERT: F 53 GLU cc_start: 0.9545 (mp0) cc_final: 0.9229 (pm20) REVERT: F 68 ASP cc_start: 0.9251 (m-30) cc_final: 0.8870 (m-30) REVERT: G 56 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8792 (mm-30) REVERT: L 237 MET cc_start: 0.7204 (ptp) cc_final: 0.6541 (ptt) REVERT: N 237 MET cc_start: 0.5994 (tpp) cc_final: 0.5676 (mmp) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.3884 time to fit residues: 79.3349 Evaluate side-chains 86 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 30.0000 chunk 66 optimal weight: 0.9990 chunk 146 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 25 optimal weight: 0.3980 chunk 121 optimal weight: 50.0000 chunk 162 optimal weight: 50.0000 chunk 139 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 HIS N 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.073895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.044002 restraints weight = 205468.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.044225 restraints weight = 108986.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.044973 restraints weight = 68652.963| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.8441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20343 Z= 0.144 Angle : 0.540 10.579 28958 Z= 0.310 Chirality : 0.036 0.163 3247 Planarity : 0.004 0.045 2533 Dihedral : 29.131 172.588 5455 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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 (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: 1.71 (0.21), residues: 1530 helix: 2.19 (0.20), residues: 624 sheet: 1.12 (0.31), residues: 268 loop : 0.14 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 146 HIS 0.004 0.001 HIS L 193 PHE 0.012 0.001 PHE E 104 TYR 0.030 0.001 TYR H 80 ARG 0.006 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 1059) hydrogen bonds : angle 3.59843 ( 2621) covalent geometry : bond 0.00308 (20343) covalent geometry : angle 0.53999 (28958) *********************** 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 114 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8816 (tp30) cc_final: 0.8162 (tp30) REVERT: A 84 PHE cc_start: 0.8909 (m-10) cc_final: 0.8633 (m-10) REVERT: A 105 GLU cc_start: 0.9414 (tp30) cc_final: 0.9026 (tm-30) REVERT: A 120 MET cc_start: 0.7463 (mmm) cc_final: 0.6918 (mmm) REVERT: B 50 ILE cc_start: 0.9266 (mm) cc_final: 0.8892 (mm) REVERT: B 53 GLU cc_start: 0.9180 (mp0) cc_final: 0.8917 (mp0) REVERT: B 63 GLU cc_start: 0.9315 (pt0) cc_final: 0.8720 (pp20) REVERT: B 68 ASP cc_start: 0.9185 (m-30) cc_final: 0.8979 (m-30) REVERT: B 85 ASP cc_start: 0.9197 (m-30) cc_final: 0.8287 (t70) REVERT: D 59 MET cc_start: 0.9626 (mmp) cc_final: 0.9361 (mmm) REVERT: D 65 ASP cc_start: 0.9431 (t0) cc_final: 0.9191 (t0) REVERT: D 66 ILE cc_start: 0.9695 (mm) cc_final: 0.9494 (mm) REVERT: E 90 MET cc_start: 0.9485 (mmp) cc_final: 0.9215 (mmm) REVERT: E 97 GLU cc_start: 0.9030 (pp20) cc_final: 0.8787 (pp20) REVERT: E 106 ASP cc_start: 0.8974 (m-30) cc_final: 0.8568 (p0) REVERT: E 110 CYS cc_start: 0.9570 (t) cc_final: 0.9256 (p) REVERT: F 50 ILE cc_start: 0.8739 (mm) cc_final: 0.8299 (mm) REVERT: F 53 GLU cc_start: 0.9549 (mp0) cc_final: 0.9224 (pm20) REVERT: F 68 ASP cc_start: 0.9270 (m-30) cc_final: 0.8905 (m-30) REVERT: G 56 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8812 (mm-30) REVERT: K 246 MET cc_start: 0.4568 (mtm) cc_final: 0.4044 (ptp) REVERT: N 237 MET cc_start: 0.5619 (tpp) cc_final: 0.5347 (mmp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.3145 time to fit residues: 58.0032 Evaluate side-chains 83 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 137 optimal weight: 6.9990 chunk 134 optimal weight: 0.0040 chunk 10 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 124 optimal weight: 50.0000 chunk 83 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 235 ASN M 100 GLN N 233 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.070789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.041285 restraints weight = 211287.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.040162 restraints weight = 119416.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.040511 restraints weight = 77517.805| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.9398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 20343 Z= 0.213 Angle : 0.610 11.382 28958 Z= 0.347 Chirality : 0.038 0.210 3247 Planarity : 0.006 0.178 2533 Dihedral : 29.133 174.743 5455 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: 1.51 (0.21), residues: 1530 helix: 1.91 (0.20), residues: 625 sheet: 1.19 (0.32), residues: 264 loop : 0.09 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 146 HIS 0.009 0.001 HIS F 75 PHE 0.018 0.002 PHE E 104 TYR 0.029 0.002 TYR H 80 ARG 0.016 0.001 ARG L 196 Details of bonding type rmsd hydrogen bonds : bond 0.06614 ( 1059) hydrogen bonds : angle 3.91266 ( 2621) covalent geometry : bond 0.00466 (20343) covalent geometry : angle 0.60973 (28958) *********************** 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 105 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.668 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: 0.9007 (m-10) cc_final: 0.8739 (m-80) REVERT: A 105 GLU cc_start: 0.9397 (tp30) cc_final: 0.9102 (tm-30) REVERT: A 120 MET cc_start: 0.8030 (mmm) cc_final: 0.7534 (mmm) REVERT: B 50 ILE cc_start: 0.9286 (mm) cc_final: 0.8952 (mm) REVERT: B 53 GLU cc_start: 0.9302 (mp0) cc_final: 0.9050 (mp0) REVERT: B 85 ASP cc_start: 0.9266 (m-30) cc_final: 0.8486 (t70) REVERT: D 59 MET cc_start: 0.9713 (mmp) cc_final: 0.9513 (mmm) REVERT: E 106 ASP cc_start: 0.9047 (m-30) cc_final: 0.8733 (p0) REVERT: E 110 CYS cc_start: 0.9529 (t) cc_final: 0.9327 (p) REVERT: F 50 ILE cc_start: 0.8655 (mm) cc_final: 0.8257 (mm) REVERT: F 53 GLU cc_start: 0.9586 (mp0) cc_final: 0.9240 (pm20) REVERT: F 63 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8906 (mt-10) REVERT: F 68 ASP cc_start: 0.9202 (m-30) cc_final: 0.8894 (m-30) REVERT: G 56 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8777 (mm-30) REVERT: K 246 MET cc_start: 0.4643 (mtm) cc_final: 0.4124 (ptp) REVERT: M 246 MET cc_start: 0.1822 (mtm) cc_final: 0.1610 (mtt) REVERT: N 237 MET cc_start: 0.6123 (tpp) cc_final: 0.5862 (mmp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2973 time to fit residues: 49.9778 Evaluate side-chains 80 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 125 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 0.0170 chunk 107 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.071607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.040910 restraints weight = 209616.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.041312 restraints weight = 115532.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.041742 restraints weight = 70380.110| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.9551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20343 Z= 0.142 Angle : 0.552 10.267 28958 Z= 0.317 Chirality : 0.037 0.173 3247 Planarity : 0.004 0.037 2533 Dihedral : 29.171 176.870 5455 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: 1.55 (0.21), residues: 1530 helix: 1.97 (0.21), residues: 625 sheet: 1.24 (0.31), residues: 264 loop : 0.06 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 146 HIS 0.003 0.001 HIS E 113 PHE 0.024 0.001 PHE E 67 TYR 0.026 0.001 TYR H 80 ARG 0.010 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 1059) hydrogen bonds : angle 3.72372 ( 2621) covalent geometry : bond 0.00299 (20343) covalent geometry : angle 0.55173 (28958) ********************** 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 110 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9504 (mp0) cc_final: 0.9240 (mp0) REVERT: A 84 PHE cc_start: 0.8964 (m-10) cc_final: 0.8628 (m-10) REVERT: A 105 GLU cc_start: 0.9352 (tp30) cc_final: 0.9102 (tm-30) REVERT: A 120 MET cc_start: 0.7784 (mmm) cc_final: 0.7253 (mmm) REVERT: B 50 ILE cc_start: 0.9305 (mm) cc_final: 0.8938 (mm) REVERT: B 53 GLU cc_start: 0.9314 (mp0) cc_final: 0.9059 (mp0) REVERT: B 63 GLU cc_start: 0.9408 (mt-10) cc_final: 0.9172 (mt-10) REVERT: B 68 ASP cc_start: 0.9194 (m-30) cc_final: 0.8977 (m-30) REVERT: B 85 ASP cc_start: 0.9177 (m-30) cc_final: 0.8417 (t70) REVERT: D 59 MET cc_start: 0.9767 (mmp) cc_final: 0.9540 (mmm) REVERT: E 90 MET cc_start: 0.9570 (mmp) cc_final: 0.9218 (mmm) REVERT: E 106 ASP cc_start: 0.9047 (m-30) cc_final: 0.8630 (p0) REVERT: E 110 CYS cc_start: 0.9563 (t) cc_final: 0.9315 (p) REVERT: F 50 ILE cc_start: 0.8713 (mm) cc_final: 0.8311 (mm) REVERT: F 53 GLU cc_start: 0.9545 (mp0) cc_final: 0.9202 (pm20) REVERT: F 68 ASP cc_start: 0.9282 (m-30) cc_final: 0.8940 (m-30) REVERT: G 56 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8854 (mm-30) REVERT: K 246 MET cc_start: 0.4555 (mtm) cc_final: 0.3959 (mtm) REVERT: M 246 MET cc_start: 0.1639 (mtm) cc_final: 0.1413 (mtt) REVERT: N 237 MET cc_start: 0.5926 (tpp) cc_final: 0.5676 (mmp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3115 time to fit residues: 53.8983 Evaluate side-chains 84 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 87 optimal weight: 30.0000 chunk 141 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 133 optimal weight: 40.0000 chunk 83 optimal weight: 10.0000 chunk 72 optimal weight: 40.0000 chunk 31 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN F 25 ASN F 75 HIS ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.061304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.030563 restraints weight = 186799.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.031014 restraints weight = 110547.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.031131 restraints weight = 78495.878| |-----------------------------------------------------------------------------| r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 1.0465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 20343 Z= 0.272 Angle : 0.668 14.448 28958 Z= 0.379 Chirality : 0.040 0.150 3247 Planarity : 0.005 0.058 2533 Dihedral : 29.140 178.942 5455 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 1.09 (0.21), residues: 1530 helix: 1.52 (0.20), residues: 625 sheet: 0.87 (0.31), residues: 288 loop : -0.09 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 146 HIS 0.009 0.001 HIS N 233 PHE 0.021 0.002 PHE E 104 TYR 0.027 0.002 TYR H 80 ARG 0.013 0.001 ARG E 40 Details of bonding type rmsd hydrogen bonds : bond 0.08566 ( 1059) hydrogen bonds : angle 4.27112 ( 2621) covalent geometry : bond 0.00593 (20343) covalent geometry : angle 0.66773 (28958) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9460.50 seconds wall clock time: 165 minutes 57.07 seconds (9957.07 seconds total)