Starting phenix.real_space_refine on Tue Nov 19 06:12:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzx_33533/11_2024/7xzx_33533.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzx_33533/11_2024/7xzx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzx_33533/11_2024/7xzx_33533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzx_33533/11_2024/7xzx_33533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzx_33533/11_2024/7xzx_33533.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzx_33533/11_2024/7xzx_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-5513/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: 10.68, per 1000 atoms: 0.55 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: 4.81 Conformation dependent library (CDL) restraints added in 1.9 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: 8.43 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: 7.93 Time building geometry restraints manager: 5.57 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: 0.590 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: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 48.110 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.370 ------------------------------------------------------------------------------- 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= 0.370 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 *********************** 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 : 1.647 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: 0.3582 time to fit residues: 139.6731 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 : 1.629 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4260 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= 0.350 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 *********************** 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 : 1.631 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: 0.7681 (mt) cc_final: 0.7476 (pt) REVERT: A 73 GLU cc_start: 0.8445 (tp30) cc_final: 0.7981 (tp30) REVERT: A 82 LEU cc_start: 0.8015 (mm) cc_final: 0.7809 (mm) REVERT: A 106 ASP cc_start: 0.8817 (m-30) cc_final: 0.8599 (m-30) REVERT: B 63 GLU cc_start: 0.8898 (pt0) cc_final: 0.8404 (pp20) REVERT: D 49 THR cc_start: 0.6658 (m) cc_final: 0.6259 (m) REVERT: D 59 MET cc_start: 0.9197 (mmp) cc_final: 0.8918 (mmm) REVERT: E 105 GLU cc_start: 0.8835 (tp30) cc_final: 0.8378 (tm-30) REVERT: K 243 MET cc_start: 0.3946 (ptp) cc_final: 0.3195 (ptt) REVERT: L 160 MET cc_start: 0.4341 (ttm) cc_final: 0.2268 (ptm) outliers start: 4 outliers final: 1 residues processed: 179 average time/residue: 0.3134 time to fit residues: 86.1509 Evaluate side-chains 118 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 178 optimal weight: 50.0000 chunk 147 optimal weight: 50.0000 chunk 164 optimal weight: 50.0000 chunk 56 optimal weight: 0.0670 chunk 132 optimal weight: 3.9990 overall best weight: 5.2126 ------------------------------------------------------------------------------- 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** A 108 ASN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4540 moved from start: 0.5192 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= 0.287 Angle : 0.682 10.988 28958 Z= 0.388 Chirality : 0.042 0.272 3247 Planarity : 0.005 0.052 2533 Dihedral : 29.708 161.697 5455 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.22 % Allowed : 2.52 % Favored : 97.25 % 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: 1.27 (0.20), residues: 1530 helix: 1.60 (0.19), residues: 626 sheet: 0.50 (0.27), residues: 320 loop : 0.36 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 146 HIS 0.011 0.002 HIS L 178 PHE 0.028 0.002 PHE K 134 TYR 0.053 0.002 TYR L 205 ARG 0.051 0.001 ARG L 196 *********************** 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 151 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 1.649 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 82 LEU cc_start: 0.7932 (mm) cc_final: 0.7641 (mm) REVERT: A 106 ASP cc_start: 0.8980 (m-30) cc_final: 0.7834 (m-30) REVERT: A 120 MET cc_start: 0.7435 (tpt) cc_final: 0.6582 (mmm) REVERT: B 53 GLU cc_start: 0.9091 (mp0) cc_final: 0.8831 (mp0) REVERT: B 63 GLU cc_start: 0.9043 (pt0) cc_final: 0.8556 (pp20) REVERT: D 59 MET cc_start: 0.9395 (mmp) cc_final: 0.8969 (mmm) REVERT: D 66 ILE cc_start: 0.9307 (mm) cc_final: 0.9071 (mm) REVERT: F 63 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8834 (mt-10) REVERT: G 65 LEU cc_start: 0.9472 (tp) cc_final: 0.9257 (tp) REVERT: H 34 TYR cc_start: 0.9334 (m-10) cc_final: 0.9009 (m-10) REVERT: H 51 ILE cc_start: 0.7395 (tt) cc_final: 0.7092 (pt) REVERT: H 86 ILE cc_start: 0.9349 (mm) cc_final: 0.9098 (mm) REVERT: L 160 MET cc_start: 0.4725 (ttm) cc_final: 0.2763 (ptm) outliers start: 3 outliers final: 1 residues processed: 151 average time/residue: 0.3054 time to fit residues: 74.2034 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 : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.5980 chunk 124 optimal weight: 30.0000 chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 200 ASN N 233 HIS N 235 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4635 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 20343 Z= 0.218 Angle : 0.578 7.867 28958 Z= 0.336 Chirality : 0.038 0.183 3247 Planarity : 0.004 0.036 2533 Dihedral : 29.375 163.319 5455 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.41 (0.21), residues: 1530 helix: 1.76 (0.20), residues: 627 sheet: 0.66 (0.27), residues: 324 loop : 0.32 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 146 HIS 0.005 0.001 HIS M 178 PHE 0.015 0.002 PHE F 61 TYR 0.040 0.002 TYR H 80 ARG 0.018 0.001 ARG C 32 *********************** 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 138 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.9173 (mp0) cc_final: 0.8927 (mp0) REVERT: B 63 GLU cc_start: 0.9015 (pt0) cc_final: 0.8491 (pp20) REVERT: D 59 MET cc_start: 0.9473 (mmp) cc_final: 0.9143 (mmm) REVERT: E 97 GLU cc_start: 0.8447 (pp20) cc_final: 0.8230 (pp20) REVERT: F 63 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8849 (mp0) REVERT: G 65 LEU cc_start: 0.9476 (tp) cc_final: 0.9234 (tp) REVERT: L 160 MET cc_start: 0.4446 (ttm) cc_final: 0.2450 (ptm) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.3008 time to fit residues: 66.2169 Evaluate side-chains 104 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 50.0000 chunk 99 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 72 optimal weight: 40.0000 chunk 150 optimal weight: 40.0000 chunk 121 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 89 optimal weight: 30.0000 chunk 157 optimal weight: 50.0000 chunk 44 optimal weight: 6.9990 overall best weight: 11.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 68 ASN K 100 GLN K 200 ASN ** L 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5100 moved from start: 0.8582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.158 20343 Z= 0.479 Angle : 0.839 14.248 28958 Z= 0.472 Chirality : 0.046 0.223 3247 Planarity : 0.009 0.260 2533 Dihedral : 29.863 167.641 5455 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % 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: 0.53 (0.20), residues: 1530 helix: 0.63 (0.19), residues: 625 sheet: 0.69 (0.30), residues: 284 loop : 0.09 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 146 HIS 0.030 0.002 HIS M 193 PHE 0.029 0.003 PHE E 104 TYR 0.033 0.003 TYR H 80 ARG 0.015 0.001 ARG E 63 *********************** 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 104 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.522 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: 0.8643 (tm-30) cc_final: 0.8241 (tm-30) REVERT: A 120 MET cc_start: 0.8610 (tpt) cc_final: 0.8100 (mmm) REVERT: B 63 GLU cc_start: 0.9088 (pt0) cc_final: 0.8663 (pp20) REVERT: E 77 ASP cc_start: 0.9418 (m-30) cc_final: 0.9211 (m-30) REVERT: E 90 MET cc_start: 0.9376 (mmp) cc_final: 0.9133 (mmm) REVERT: F 63 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8803 (mp0) REVERT: F 84 MET cc_start: 0.8738 (tpp) cc_final: 0.8418 (tpp) REVERT: L 160 MET cc_start: 0.4606 (ttm) cc_final: 0.1966 (mtm) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3073 time to fit residues: 50.2647 Evaluate side-chains 78 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 7.9990 chunk 158 optimal weight: 50.0000 chunk 34 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 146 optimal weight: 50.0000 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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** K 200 ASN M 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5042 moved from start: 0.9087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 20343 Z= 0.279 Angle : 0.635 13.008 28958 Z= 0.364 Chirality : 0.039 0.219 3247 Planarity : 0.005 0.069 2533 Dihedral : 30.040 171.683 5455 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: 0.99 (0.21), residues: 1530 helix: 1.30 (0.20), residues: 626 sheet: 0.70 (0.30), residues: 284 loop : 0.10 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 146 HIS 0.012 0.001 HIS N 178 PHE 0.013 0.002 PHE F 61 TYR 0.022 0.002 TYR F 88 ARG 0.028 0.001 ARG H 76 *********************** 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 109 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.539 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 120 MET cc_start: 0.8617 (tpt) cc_final: 0.8012 (mmm) REVERT: B 63 GLU cc_start: 0.9182 (pt0) cc_final: 0.8721 (pp20) REVERT: E 105 GLU cc_start: 0.9267 (tm-30) cc_final: 0.9067 (tm-30) REVERT: E 106 ASP cc_start: 0.8904 (p0) cc_final: 0.8671 (p0) REVERT: H 56 MET cc_start: 0.9361 (mmp) cc_final: 0.9143 (mmm) REVERT: L 160 MET cc_start: 0.4589 (ttm) cc_final: 0.1895 (mtm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2655 time to fit residues: 45.2130 Evaluate side-chains 79 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 175 optimal weight: 40.0000 chunk 109 optimal weight: 20.0000 chunk 106 optimal weight: 40.0000 chunk 80 optimal weight: 10.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 ASN K 214 HIS M 104 GLN ** M 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5150 moved from start: 0.9983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20343 Z= 0.357 Angle : 0.681 13.862 28958 Z= 0.388 Chirality : 0.041 0.226 3247 Planarity : 0.005 0.038 2533 Dihedral : 29.893 174.155 5455 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: 0.81 (0.21), residues: 1530 helix: 1.21 (0.20), residues: 632 sheet: 0.53 (0.30), residues: 288 loop : -0.05 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 146 HIS 0.008 0.002 HIS H 79 PHE 0.017 0.002 PHE E 67 TYR 0.018 0.002 TYR C 50 ARG 0.019 0.001 ARG K 290 *********************** 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 98 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8640 (tpt) cc_final: 0.8162 (mmm) REVERT: B 63 GLU cc_start: 0.9252 (pt0) cc_final: 0.8862 (pp20) REVERT: E 90 MET cc_start: 0.9394 (mmp) cc_final: 0.9103 (mmm) REVERT: E 105 GLU cc_start: 0.9359 (tm-30) cc_final: 0.9057 (tm-30) REVERT: E 106 ASP cc_start: 0.8781 (p0) cc_final: 0.8462 (p0) REVERT: F 63 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8775 (mp0) REVERT: F 84 MET cc_start: 0.8620 (tpp) cc_final: 0.8273 (tpp) REVERT: L 160 MET cc_start: 0.4476 (ttm) cc_final: 0.2296 (mtm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2989 time to fit residues: 46.4201 Evaluate side-chains 70 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 20.0000 chunk 70 optimal weight: 0.0050 chunk 104 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 0.0030 chunk 33 optimal weight: 0.8980 chunk 111 optimal weight: 20.0000 chunk 119 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 137 optimal weight: 30.0000 overall best weight: 2.7810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 ASN ** M 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5059 moved from start: 1.0076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20343 Z= 0.188 Angle : 0.588 11.646 28958 Z= 0.338 Chirality : 0.038 0.186 3247 Planarity : 0.004 0.059 2533 Dihedral : 29.799 175.695 5455 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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 (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: 1.13 (0.21), residues: 1530 helix: 1.61 (0.20), residues: 630 sheet: 0.74 (0.31), residues: 268 loop : -0.03 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 146 HIS 0.008 0.001 HIS B 75 PHE 0.012 0.001 PHE F 61 TYR 0.017 0.001 TYR L 205 ARG 0.016 0.001 ARG K 290 *********************** 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 103 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.708 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: A 41 TYR cc_start: 0.6706 (m-10) cc_final: 0.6389 (m-10) REVERT: A 120 MET cc_start: 0.8650 (tpt) cc_final: 0.8352 (mmm) REVERT: B 63 GLU cc_start: 0.9225 (pt0) cc_final: 0.8736 (pp20) REVERT: B 85 ASP cc_start: 0.9021 (m-30) cc_final: 0.8188 (t70) REVERT: E 90 MET cc_start: 0.9366 (mmp) cc_final: 0.9007 (mmm) REVERT: E 105 GLU cc_start: 0.9392 (tm-30) cc_final: 0.9146 (tm-30) REVERT: F 50 ILE cc_start: 0.8557 (mm) cc_final: 0.8295 (mm) REVERT: F 74 GLU cc_start: 0.8622 (tp30) cc_final: 0.8301 (tm-30) REVERT: G 56 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8837 (mm-30) REVERT: L 160 MET cc_start: 0.4031 (ttm) cc_final: 0.1697 (mtm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3218 time to fit residues: 51.9067 Evaluate side-chains 82 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 128 optimal weight: 40.0000 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 162 optimal weight: 40.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 ASN L 235 ASN ** M 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5079 moved from start: 1.0328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20343 Z= 0.215 Angle : 0.586 11.476 28958 Z= 0.337 Chirality : 0.038 0.172 3247 Planarity : 0.004 0.039 2533 Dihedral : 29.538 176.085 5455 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: 1.19 (0.21), residues: 1530 helix: 1.71 (0.20), residues: 630 sheet: 0.78 (0.31), residues: 268 loop : -0.07 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 146 HIS 0.008 0.001 HIS N 233 PHE 0.012 0.001 PHE F 61 TYR 0.015 0.001 TYR L 205 ARG 0.008 0.000 ARG C 29 *********************** 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 99 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.749 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 120 MET cc_start: 0.8630 (tpt) cc_final: 0.8366 (mmm) REVERT: B 63 GLU cc_start: 0.9209 (pt0) cc_final: 0.8758 (pp20) REVERT: B 85 ASP cc_start: 0.9035 (m-30) cc_final: 0.8303 (t70) REVERT: D 59 MET cc_start: 0.9669 (mmp) cc_final: 0.9461 (mmm) REVERT: E 90 MET cc_start: 0.9364 (mmp) cc_final: 0.9001 (mmm) REVERT: E 105 GLU cc_start: 0.9423 (tm-30) cc_final: 0.9183 (tm-30) REVERT: F 68 ASP cc_start: 0.9191 (m-30) cc_final: 0.8980 (m-30) REVERT: G 56 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8739 (mm-30) REVERT: L 160 MET cc_start: 0.4228 (ttm) cc_final: 0.1852 (mtm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3067 time to fit residues: 48.0988 Evaluate side-chains 79 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.0770 chunk 172 optimal weight: 0.0060 chunk 105 optimal weight: 40.0000 chunk 82 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 181 optimal weight: 50.0000 chunk 166 optimal weight: 10.0000 chunk 144 optimal weight: 50.0000 chunk 14 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 88 optimal weight: 40.0000 overall best weight: 5.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 HIS F 75 HIS ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 ASN ** M 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5114 moved from start: 1.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20343 Z= 0.240 Angle : 0.611 12.593 28958 Z= 0.349 Chirality : 0.038 0.222 3247 Planarity : 0.005 0.042 2533 Dihedral : 29.474 178.903 5455 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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 (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: 1.02 (0.21), residues: 1530 helix: 1.60 (0.20), residues: 629 sheet: 0.69 (0.31), residues: 288 loop : -0.24 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 146 HIS 0.007 0.001 HIS N 233 PHE 0.011 0.001 PHE F 61 TYR 0.015 0.001 TYR D 34 ARG 0.009 0.001 ARG K 290 ********************** 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 94 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.746 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 120 MET cc_start: 0.8690 (tpt) cc_final: 0.8342 (mmm) REVERT: B 85 ASP cc_start: 0.9052 (m-30) cc_final: 0.8323 (t70) REVERT: D 59 MET cc_start: 0.9658 (mmp) cc_final: 0.9436 (mmm) REVERT: E 90 MET cc_start: 0.9391 (mmp) cc_final: 0.8980 (mmm) REVERT: E 105 GLU cc_start: 0.9448 (tm-30) cc_final: 0.9189 (tm-30) REVERT: F 68 ASP cc_start: 0.9208 (m-30) cc_final: 0.8919 (m-30) REVERT: F 84 MET cc_start: 0.8437 (tpp) cc_final: 0.8062 (tpt) REVERT: L 160 MET cc_start: 0.4065 (ttm) cc_final: 0.2268 (mtm) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2904 time to fit residues: 44.0533 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 : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 50.0000 chunk 153 optimal weight: 0.0050 chunk 44 optimal weight: 0.9990 chunk 133 optimal weight: 50.0000 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 144 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 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 = 0.3555 r_free = 0.3555 target = 0.062830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.031462 restraints weight = 177528.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.031800 restraints weight = 103274.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.031933 restraints weight = 72299.567| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 1.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20343 Z= 0.172 Angle : 0.576 10.693 28958 Z= 0.330 Chirality : 0.038 0.184 3247 Planarity : 0.004 0.040 2533 Dihedral : 29.374 179.194 5455 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: 1.13 (0.21), residues: 1530 helix: 1.74 (0.20), residues: 628 sheet: 0.76 (0.31), residues: 288 loop : -0.22 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 146 HIS 0.007 0.001 HIS N 233 PHE 0.015 0.001 PHE G 25 TYR 0.013 0.001 TYR L 205 ARG 0.007 0.000 ARG K 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3020.82 seconds wall clock time: 69 minutes 33.83 seconds (4173.83 seconds total)