Starting phenix.real_space_refine on Tue Feb 13 22:27:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lo8_0935/02_2024/6lo8_0935.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lo8_0935/02_2024/6lo8_0935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lo8_0935/02_2024/6lo8_0935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lo8_0935/02_2024/6lo8_0935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lo8_0935/02_2024/6lo8_0935.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lo8_0935/02_2024/6lo8_0935.pdb" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5075 2.51 5 N 1348 2.21 5 O 1486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 151": "OD1" <-> "OD2" Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 167": "OD1" <-> "OD2" Residue "D PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "D ASP 173": "OD1" <-> "OD2" Residue "E GLU 17": "OE1" <-> "OE2" Residue "E ASP 23": "OD1" <-> "OD2" Residue "E ASP 38": "OD1" <-> "OD2" Residue "F ASP 27": "OD1" <-> "OD2" Residue "F PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 11": "OE1" <-> "OE2" Residue "G PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 42": "OD1" <-> "OD2" Residue "G PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 25": "OE1" <-> "OE2" Residue "H ASP 31": "OD1" <-> "OD2" Residue "H GLU 51": "OE1" <-> "OE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 38": "OD1" <-> "OD2" Residue "J ASP 27": "OD1" <-> "OD2" Residue "J PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7972 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 938 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 1 Chain: "B" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1440 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain breaks: 3 Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 859 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 107} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 984 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "E" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 661 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "F" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 660 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "G" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 618 Classifications: {'peptide': 74} Link IDs: {'TRANS': 73} Chain: "H" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 581 Classifications: {'peptide': 74} Link IDs: {'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 661 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "J" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 570 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 4.69, per 1000 atoms: 0.59 Number of scatterers: 7972 At special positions: 0 Unit cell: (132.93, 104.445, 106.555, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1486 8.00 N 1348 7.00 C 5075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 141 " distance=1.79 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 59 " distance=2.03 Simple disulfide: pdb=" SG CYS E 39 " - pdb=" SG CYS E 55 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 66 " distance=2.03 Simple disulfide: pdb=" SG CYS F 44 " - pdb=" SG CYS F 62 " distance=2.02 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 59 " distance=2.04 Simple disulfide: pdb=" SG CYS G 39 " - pdb=" SG CYS G 55 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 65 " distance=2.03 Simple disulfide: pdb=" SG CYS H 44 " - pdb=" SG CYS H 61 " distance=2.03 Simple disulfide: pdb=" SG CYS I 35 " - pdb=" SG CYS I 59 " distance=2.03 Simple disulfide: pdb=" SG CYS I 39 " - pdb=" SG CYS I 55 " distance=2.01 Simple disulfide: pdb=" SG CYS J 40 " - pdb=" SG CYS J 65 " distance=2.03 Simple disulfide: pdb=" SG CYS J 44 " - pdb=" SG CYS J 61 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.9 seconds 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1860 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 80.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 25 through 41 Processing helix chain 'A' and resid 42 through 65 removed outlier: 3.622A pdb=" N SER A 46 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 146 Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.998A pdb=" N PHE A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 195 Processing helix chain 'B' and resid 37 through 62 Processing helix chain 'B' and resid 62 through 71 Processing helix chain 'B' and resid 99 through 116 removed outlier: 4.063A pdb=" N TYR B 109 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 130 through 148 Processing helix chain 'B' and resid 244 through 261 removed outlier: 3.607A pdb=" N LEU B 260 " --> pdb=" O HIS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 395 through 412 Processing helix chain 'C' and resid 88 through 120 removed outlier: 4.060A pdb=" N PHE C 114 " --> pdb=" O PHE C 110 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY C 118 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 137 removed outlier: 3.555A pdb=" N PHE C 137 " --> pdb=" O TYR C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 167 removed outlier: 3.959A pdb=" N ALA C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE C 155 " --> pdb=" O TYR C 151 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 198 removed outlier: 3.598A pdb=" N ARG C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 93 Proline residue: D 91 - end of helix Processing helix chain 'D' and resid 93 through 103 removed outlier: 3.765A pdb=" N PHE D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 102 " --> pdb=" O TYR D 98 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 134 Processing helix chain 'D' and resid 140 through 166 removed outlier: 3.784A pdb=" N LYS D 144 " --> pdb=" O PRO D 140 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 180 Processing helix chain 'E' and resid 8 through 40 removed outlier: 3.777A pdb=" N PHE E 12 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N CYS E 39 " --> pdb=" O CYS E 35 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL E 40 " --> pdb=" O PHE E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 81 removed outlier: 3.601A pdb=" N ALA E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 45 removed outlier: 3.544A pdb=" N THR F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS F 44 " --> pdb=" O CYS F 40 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE F 45 " --> pdb=" O LEU F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 84 removed outlier: 4.038A pdb=" N GLN F 82 " --> pdb=" O GLY F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 92 Processing helix chain 'F' and resid 93 through 98 removed outlier: 3.719A pdb=" N ARG F 97 " --> pdb=" O HIS F 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 39 removed outlier: 4.212A pdb=" N CYS G 39 " --> pdb=" O CYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 80 removed outlier: 3.569A pdb=" N ALA G 80 " --> pdb=" O GLU G 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 44 removed outlier: 3.767A pdb=" N LEU H 26 " --> pdb=" O ALA H 22 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL H 29 " --> pdb=" O GLU H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.596A pdb=" N SER H 60 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 38 Processing helix chain 'I' and resid 49 through 81 removed outlier: 3.941A pdb=" N ALA I 80 " --> pdb=" O GLU I 76 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU I 81 " --> pdb=" O GLN I 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 44 removed outlier: 3.758A pdb=" N GLU J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS J 44 " --> pdb=" O CYS J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 83 removed outlier: 4.003A pdb=" N ASP J 63 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN J 81 " --> pdb=" O GLY J 77 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET J 83 " --> pdb=" O ASN J 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 88 through 91 Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 241 removed outlier: 6.975A pdb=" N VAL B 240 " --> pdb=" O VAL B 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 611 hydrogen bonds defined for protein. 1827 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1324 1.32 - 1.45: 2170 1.45 - 1.57: 4530 1.57 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 8117 Sorted by residual: bond pdb=" N PRO A 43 " pdb=" CD PRO A 43 " ideal model delta sigma weight residual 1.473 1.542 -0.069 1.40e-02 5.10e+03 2.43e+01 bond pdb=" C CYS I 55 " pdb=" O CYS I 55 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.43e+01 bond pdb=" CA ASN G 41 " pdb=" C ASN G 41 " ideal model delta sigma weight residual 1.522 1.563 -0.042 1.72e-02 3.38e+03 5.85e+00 bond pdb=" CA CYS I 55 " pdb=" C CYS I 55 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.30e-02 5.92e+03 5.05e+00 bond pdb=" CA ILE I 56 " pdb=" CB ILE I 56 " ideal model delta sigma weight residual 1.543 1.506 0.037 1.66e-02 3.63e+03 4.94e+00 ... (remaining 8112 not shown) Histogram of bond angle deviations from ideal: 98.16 - 105.39: 115 105.39 - 112.63: 4055 112.63 - 119.86: 3001 119.86 - 127.09: 3673 127.09 - 134.33: 59 Bond angle restraints: 10903 Sorted by residual: angle pdb=" N SER A 46 " pdb=" CA SER A 46 " pdb=" C SER A 46 " ideal model delta sigma weight residual 111.36 119.92 -8.56 1.09e+00 8.42e-01 6.16e+01 angle pdb=" N PRO A 43 " pdb=" CA PRO A 43 " pdb=" C PRO A 43 " ideal model delta sigma weight residual 112.47 98.37 14.10 2.06e+00 2.36e-01 4.69e+01 angle pdb=" N CYS I 39 " pdb=" CA CYS I 39 " pdb=" C CYS I 39 " ideal model delta sigma weight residual 112.94 122.20 -9.26 1.41e+00 5.03e-01 4.32e+01 angle pdb=" N ASP I 38 " pdb=" CA ASP I 38 " pdb=" C ASP I 38 " ideal model delta sigma weight residual 111.36 118.30 -6.94 1.09e+00 8.42e-01 4.06e+01 angle pdb=" N CYS A 42 " pdb=" CA CYS A 42 " pdb=" C CYS A 42 " ideal model delta sigma weight residual 109.81 122.37 -12.56 2.21e+00 2.05e-01 3.23e+01 ... (remaining 10898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 4298 16.54 - 33.09: 497 33.09 - 49.63: 95 49.63 - 66.18: 25 66.18 - 82.72: 13 Dihedral angle restraints: 4928 sinusoidal: 2038 harmonic: 2890 Sorted by residual: dihedral pdb=" CB CYS I 39 " pdb=" SG CYS I 39 " pdb=" SG CYS I 55 " pdb=" CB CYS I 55 " ideal model delta sinusoidal sigma weight residual 93.00 15.45 77.55 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS H 44 " pdb=" SG CYS H 44 " pdb=" SG CYS H 61 " pdb=" CB CYS H 61 " ideal model delta sinusoidal sigma weight residual 93.00 168.96 -75.96 1 1.00e+01 1.00e-02 7.27e+01 dihedral pdb=" CB CYS J 44 " pdb=" SG CYS J 44 " pdb=" SG CYS J 61 " pdb=" CB CYS J 61 " ideal model delta sinusoidal sigma weight residual -86.00 -147.78 61.78 1 1.00e+01 1.00e-02 5.06e+01 ... (remaining 4925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1033 0.068 - 0.136: 130 0.136 - 0.204: 17 0.204 - 0.272: 3 0.272 - 0.340: 2 Chirality restraints: 1185 Sorted by residual: chirality pdb=" CA CYS I 39 " pdb=" N CYS I 39 " pdb=" C CYS I 39 " pdb=" CB CYS I 39 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA ILE I 56 " pdb=" N ILE I 56 " pdb=" C ILE I 56 " pdb=" CB ILE I 56 " both_signs ideal model delta sigma weight residual False 2.43 2.13 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA CYS I 35 " pdb=" N CYS I 35 " pdb=" C CYS I 35 " pdb=" CB CYS I 35 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1182 not shown) Planarity restraints: 1392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 42 " -0.096 5.00e-02 4.00e+02 1.46e-01 3.41e+01 pdb=" N PRO A 43 " 0.252 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR I 37 " -0.024 2.00e-02 2.50e+03 5.06e-02 2.56e+01 pdb=" C THR I 37 " 0.087 2.00e-02 2.50e+03 pdb=" O THR I 37 " -0.034 2.00e-02 2.50e+03 pdb=" N ASP I 38 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 107 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ARG B 107 " -0.056 2.00e-02 2.50e+03 pdb=" O ARG B 107 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG B 108 " 0.019 2.00e-02 2.50e+03 ... (remaining 1389 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1694 2.77 - 3.31: 7499 3.31 - 3.84: 13253 3.84 - 4.37: 14273 4.37 - 4.90: 25404 Nonbonded interactions: 62123 Sorted by model distance: nonbonded pdb=" OG SER D 71 " pdb=" O SER D 128 " model vdw 2.242 2.440 nonbonded pdb=" O MET A 36 " pdb=" OG1 THR A 40 " model vdw 2.297 2.440 nonbonded pdb=" O GLU I 33 " pdb=" OG1 THR I 37 " model vdw 2.309 2.440 nonbonded pdb=" OH TYR A 136 " pdb=" OG SER A 186 " model vdw 2.315 2.440 nonbonded pdb=" O ASP E 42 " pdb=" NZ LYS J 68 " model vdw 2.318 2.520 ... (remaining 62118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'E' and resid 7 through 80) selection = chain 'G' selection = (chain 'I' and resid 7 through 80) } ncs_group { reference = (chain 'H' and resid 14 through 86) selection = chain 'J' } 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=1.00 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: 2.000 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: 6.790 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 24.280 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8117 Z= 0.315 Angle : 0.865 14.104 10903 Z= 0.496 Chirality : 0.049 0.340 1185 Planarity : 0.007 0.146 1392 Dihedral : 14.877 82.722 3029 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.72 % Favored : 96.07 % Rotamer: Outliers : 0.46 % Allowed : 7.10 % Favored : 92.44 % 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: -3.08 (0.21), residues: 967 helix: -1.56 (0.14), residues: 753 sheet: -0.91 (0.97), residues: 22 loop : -3.38 (0.34), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 106 HIS 0.009 0.002 HIS C 156 PHE 0.023 0.002 PHE D 65 TYR 0.014 0.002 TYR C 133 ARG 0.005 0.000 ARG I 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 332 time to evaluate : 1.044 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 56 LEU cc_start: 0.8288 (mp) cc_final: 0.8030 (pp) REVERT: A 129 PHE cc_start: 0.7855 (m-80) cc_final: 0.7170 (m-10) REVERT: A 189 ILE cc_start: 0.9155 (mm) cc_final: 0.8867 (mm) REVERT: B 39 MET cc_start: 0.4281 (mtm) cc_final: 0.3602 (tmm) REVERT: B 42 TRP cc_start: 0.7701 (m100) cc_final: 0.7003 (m-10) REVERT: B 82 LYS cc_start: 0.8166 (mmpt) cc_final: 0.7807 (tptt) REVERT: C 108 TYR cc_start: 0.8142 (m-80) cc_final: 0.7629 (m-80) REVERT: C 175 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8646 (tttt) REVERT: D 82 GLU cc_start: 0.8368 (tp30) cc_final: 0.8101 (tp30) REVERT: D 123 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8063 (tm-30) REVERT: D 130 ILE cc_start: 0.9328 (tt) cc_final: 0.9128 (tt) REVERT: D 165 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8446 (mm-30) REVERT: G 28 TYR cc_start: 0.8880 (t80) cc_final: 0.8585 (t80) REVERT: H 19 ILE cc_start: 0.9291 (tt) cc_final: 0.8881 (tp) REVERT: H 36 LEU cc_start: 0.9542 (tp) cc_final: 0.9313 (tp) REVERT: H 39 ASN cc_start: 0.8650 (m-40) cc_final: 0.7616 (m110) REVERT: I 17 GLU cc_start: 0.8570 (tp30) cc_final: 0.8214 (tp30) REVERT: I 19 LYS cc_start: 0.9305 (mmtt) cc_final: 0.8708 (mtpp) outliers start: 4 outliers final: 2 residues processed: 336 average time/residue: 0.2484 time to fit residues: 105.7179 Evaluate side-chains 232 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 230 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain I residue 35 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN F 34 ASN F 90 ASN F 91 GLN G 20 GLN G 30 ASN G 53 GLN G 72 GLN G 77 GLN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN J 20 GLN J 34 ASN ** J 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8117 Z= 0.281 Angle : 0.713 13.222 10903 Z= 0.381 Chirality : 0.039 0.172 1185 Planarity : 0.005 0.088 1392 Dihedral : 5.543 47.416 1075 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.24 % Favored : 95.66 % Rotamer: Outliers : 3.44 % Allowed : 16.84 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: -0.43 (0.25), residues: 967 helix: 0.42 (0.17), residues: 761 sheet: -0.14 (1.09), residues: 22 loop : -3.08 (0.37), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 106 HIS 0.005 0.001 HIS B 65 PHE 0.012 0.001 PHE C 110 TYR 0.013 0.001 TYR H 49 ARG 0.004 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 263 time to evaluate : 1.084 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 56 LEU cc_start: 0.8280 (mp) cc_final: 0.7992 (pp) REVERT: A 129 PHE cc_start: 0.7979 (m-80) cc_final: 0.7333 (m-80) REVERT: B 39 MET cc_start: 0.4250 (mtm) cc_final: 0.3661 (tmm) REVERT: B 67 THR cc_start: 0.8557 (m) cc_final: 0.8256 (p) REVERT: B 82 LYS cc_start: 0.8310 (mmpt) cc_final: 0.7837 (tptt) REVERT: C 163 HIS cc_start: 0.8784 (OUTLIER) cc_final: 0.8578 (t70) REVERT: D 82 GLU cc_start: 0.8320 (tp30) cc_final: 0.8078 (pp20) REVERT: D 111 ASP cc_start: 0.7220 (t0) cc_final: 0.6583 (t0) REVERT: D 123 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8105 (tm-30) REVERT: D 144 LYS cc_start: 0.8452 (tttt) cc_final: 0.8111 (pttm) REVERT: D 155 MET cc_start: 0.7914 (mmp) cc_final: 0.7676 (mmt) REVERT: D 165 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8393 (mm-30) REVERT: E 64 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8255 (mm) REVERT: F 27 ASP cc_start: 0.8616 (m-30) cc_final: 0.8297 (m-30) REVERT: F 29 MET cc_start: 0.7938 (mtp) cc_final: 0.7654 (mtt) REVERT: F 84 ARG cc_start: 0.8692 (tpp-160) cc_final: 0.8369 (tpp80) REVERT: G 21 MET cc_start: 0.7822 (tpp) cc_final: 0.7502 (tpp) REVERT: G 22 LYS cc_start: 0.8930 (tptp) cc_final: 0.8615 (tptt) REVERT: G 25 MET cc_start: 0.7973 (mtp) cc_final: 0.7452 (mtp) REVERT: H 62 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8694 (mm) REVERT: I 17 GLU cc_start: 0.8618 (tp30) cc_final: 0.8315 (tp30) REVERT: I 35 CYS cc_start: 0.6071 (m) cc_final: 0.5861 (m) outliers start: 30 outliers final: 18 residues processed: 281 average time/residue: 0.2283 time to fit residues: 83.6593 Evaluate side-chains 245 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 224 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 25 GLU Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 86 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN F 94 HIS G 20 GLN H 17 GLN ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8117 Z= 0.212 Angle : 0.669 15.218 10903 Z= 0.352 Chirality : 0.038 0.177 1185 Planarity : 0.004 0.067 1392 Dihedral : 5.238 42.640 1074 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.45 % Rotamer: Outliers : 3.89 % Allowed : 18.90 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.59 (0.26), residues: 967 helix: 1.18 (0.18), residues: 761 sheet: 0.02 (1.06), residues: 22 loop : -2.86 (0.38), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 106 HIS 0.004 0.001 HIS F 47 PHE 0.020 0.001 PHE C 187 TYR 0.016 0.001 TYR B 398 ARG 0.004 0.000 ARG I 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 256 time to evaluate : 1.055 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 56 LEU cc_start: 0.8158 (mp) cc_final: 0.7900 (pp) REVERT: A 129 PHE cc_start: 0.7931 (m-80) cc_final: 0.7233 (m-10) REVERT: A 194 LYS cc_start: 0.8850 (tppp) cc_final: 0.8593 (mptt) REVERT: B 39 MET cc_start: 0.4217 (mtm) cc_final: 0.3620 (tmm) REVERT: B 67 THR cc_start: 0.8568 (m) cc_final: 0.8266 (p) REVERT: B 82 LYS cc_start: 0.8239 (mmpt) cc_final: 0.7789 (tptt) REVERT: C 107 PHE cc_start: 0.8750 (t80) cc_final: 0.8534 (t80) REVERT: C 153 PHE cc_start: 0.8816 (t80) cc_final: 0.8553 (m-80) REVERT: D 64 MET cc_start: 0.6609 (tmm) cc_final: 0.6249 (tmm) REVERT: D 78 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7961 (tm-30) REVERT: D 111 ASP cc_start: 0.7469 (t0) cc_final: 0.6944 (t0) REVERT: D 123 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8101 (tm-30) REVERT: D 155 MET cc_start: 0.7901 (mmp) cc_final: 0.7659 (mmt) REVERT: D 165 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8349 (mm-30) REVERT: E 18 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.8044 (mp10) REVERT: E 64 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8310 (mm) REVERT: F 27 ASP cc_start: 0.8607 (m-30) cc_final: 0.8256 (m-30) REVERT: F 29 MET cc_start: 0.7989 (mtp) cc_final: 0.7742 (mtt) REVERT: G 22 LYS cc_start: 0.8910 (tptp) cc_final: 0.8703 (tptt) REVERT: G 38 ASP cc_start: 0.7591 (m-30) cc_final: 0.7279 (m-30) REVERT: G 42 ASP cc_start: 0.7562 (t0) cc_final: 0.7127 (t0) REVERT: H 59 SER cc_start: 0.8646 (m) cc_final: 0.7952 (p) REVERT: H 62 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8706 (mm) REVERT: I 10 GLN cc_start: 0.8836 (mp10) cc_final: 0.8561 (mp10) REVERT: I 17 GLU cc_start: 0.8611 (tp30) cc_final: 0.8313 (tp30) outliers start: 34 outliers final: 22 residues processed: 278 average time/residue: 0.2224 time to fit residues: 80.4269 Evaluate side-chains 255 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 230 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 18 GLN Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 44 optimal weight: 0.0670 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 GLN H 75 GLN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8117 Z= 0.192 Angle : 0.659 10.103 10903 Z= 0.343 Chirality : 0.039 0.239 1185 Planarity : 0.004 0.057 1392 Dihedral : 5.123 43.035 1074 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.65 % Favored : 95.24 % Rotamer: Outliers : 3.44 % Allowed : 21.31 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 1.15 (0.26), residues: 967 helix: 1.60 (0.18), residues: 756 sheet: 0.02 (1.04), residues: 22 loop : -2.64 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 106 HIS 0.005 0.001 HIS F 94 PHE 0.015 0.001 PHE C 107 TYR 0.021 0.001 TYR C 151 ARG 0.005 0.000 ARG I 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 262 time to evaluate : 1.014 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 56 LEU cc_start: 0.8149 (mp) cc_final: 0.7870 (pp) REVERT: A 140 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 194 LYS cc_start: 0.8862 (tppp) cc_final: 0.8628 (mptt) REVERT: B 39 MET cc_start: 0.4260 (mtm) cc_final: 0.3618 (tmm) REVERT: B 67 THR cc_start: 0.8579 (m) cc_final: 0.8264 (p) REVERT: B 82 LYS cc_start: 0.8259 (mmpt) cc_final: 0.7998 (tptt) REVERT: C 153 PHE cc_start: 0.8797 (t80) cc_final: 0.8552 (m-80) REVERT: D 78 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7867 (tm-30) REVERT: D 111 ASP cc_start: 0.7710 (t0) cc_final: 0.7042 (t0) REVERT: D 123 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8086 (tm-30) REVERT: D 165 GLU cc_start: 0.8553 (mm-30) cc_final: 0.7990 (mm-30) REVERT: E 64 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8332 (mm) REVERT: F 27 ASP cc_start: 0.8622 (m-30) cc_final: 0.8297 (m-30) REVERT: F 60 GLN cc_start: 0.8396 (mt0) cc_final: 0.8111 (mt0) REVERT: G 22 LYS cc_start: 0.8894 (tptp) cc_final: 0.8622 (tptt) REVERT: G 42 ASP cc_start: 0.7626 (t0) cc_final: 0.7208 (t0) REVERT: H 59 SER cc_start: 0.8609 (m) cc_final: 0.7779 (p) REVERT: H 62 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8634 (mm) REVERT: I 10 GLN cc_start: 0.8808 (mp10) cc_final: 0.8481 (mp10) outliers start: 30 outliers final: 20 residues processed: 278 average time/residue: 0.2248 time to fit residues: 81.7858 Evaluate side-chains 250 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 228 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 0.0770 chunk 78 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 0.0050 chunk 82 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.4752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN I 30 ASN ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8117 Z= 0.192 Angle : 0.667 10.292 10903 Z= 0.345 Chirality : 0.039 0.229 1185 Planarity : 0.004 0.055 1392 Dihedral : 5.030 42.587 1074 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.76 % Favored : 95.14 % Rotamer: Outliers : 3.78 % Allowed : 23.48 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 1.34 (0.26), residues: 967 helix: 1.71 (0.18), residues: 757 sheet: 0.18 (1.07), residues: 22 loop : -2.51 (0.38), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP B 106 HIS 0.005 0.001 HIS F 94 PHE 0.033 0.001 PHE C 107 TYR 0.023 0.001 TYR C 151 ARG 0.005 0.000 ARG F 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 252 time to evaluate : 0.930 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 45 LYS cc_start: 0.8663 (mmtt) cc_final: 0.8360 (mmtm) REVERT: A 140 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7932 (tm-30) REVERT: A 194 LYS cc_start: 0.8861 (tppp) cc_final: 0.8631 (mptt) REVERT: B 39 MET cc_start: 0.4268 (mtm) cc_final: 0.3628 (tmm) REVERT: B 82 LYS cc_start: 0.8125 (mmpt) cc_final: 0.7860 (tptt) REVERT: C 153 PHE cc_start: 0.8809 (t80) cc_final: 0.8561 (m-80) REVERT: C 163 HIS cc_start: 0.8666 (OUTLIER) cc_final: 0.8023 (t70) REVERT: D 64 MET cc_start: 0.5762 (OUTLIER) cc_final: 0.5101 (tmm) REVERT: D 78 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7742 (tm-30) REVERT: D 111 ASP cc_start: 0.7709 (t0) cc_final: 0.7342 (t0) REVERT: D 123 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8087 (tm-30) REVERT: D 165 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8025 (mm-30) REVERT: E 64 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8333 (mm) REVERT: F 27 ASP cc_start: 0.8631 (m-30) cc_final: 0.8293 (m-30) REVERT: F 60 GLN cc_start: 0.8389 (mt0) cc_final: 0.8058 (mt0) REVERT: G 22 LYS cc_start: 0.8873 (tptp) cc_final: 0.8648 (tptt) REVERT: G 42 ASP cc_start: 0.7619 (t0) cc_final: 0.7229 (t0) REVERT: H 59 SER cc_start: 0.8483 (m) cc_final: 0.7920 (p) REVERT: H 62 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8571 (mm) REVERT: I 10 GLN cc_start: 0.8728 (mp10) cc_final: 0.8455 (mp10) REVERT: I 26 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7782 (ttp80) REVERT: I 52 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7585 (mt-10) outliers start: 33 outliers final: 21 residues processed: 269 average time/residue: 0.2219 time to fit residues: 77.6563 Evaluate side-chains 263 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 238 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8117 Z= 0.213 Angle : 0.681 12.336 10903 Z= 0.352 Chirality : 0.039 0.224 1185 Planarity : 0.004 0.051 1392 Dihedral : 4.994 42.705 1074 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.17 % Favored : 94.73 % Rotamer: Outliers : 4.12 % Allowed : 24.28 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 1.44 (0.26), residues: 967 helix: 1.78 (0.18), residues: 758 sheet: 0.06 (1.05), residues: 22 loop : -2.49 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 106 HIS 0.004 0.001 HIS C 163 PHE 0.034 0.001 PHE C 107 TYR 0.027 0.001 TYR C 151 ARG 0.004 0.000 ARG I 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 245 time to evaluate : 1.420 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 45 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8449 (mptt) REVERT: A 140 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7902 (tm-30) REVERT: B 39 MET cc_start: 0.4337 (mtm) cc_final: 0.3664 (tmm) REVERT: B 82 LYS cc_start: 0.8267 (mmpt) cc_final: 0.7954 (tptt) REVERT: C 153 PHE cc_start: 0.8886 (t80) cc_final: 0.8616 (m-80) REVERT: C 163 HIS cc_start: 0.8524 (OUTLIER) cc_final: 0.7879 (t70) REVERT: D 64 MET cc_start: 0.5630 (OUTLIER) cc_final: 0.5148 (tmm) REVERT: D 78 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7829 (tm-30) REVERT: D 111 ASP cc_start: 0.7784 (t0) cc_final: 0.7181 (t0) REVERT: D 123 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8107 (tm-30) REVERT: D 155 MET cc_start: 0.7682 (mmt) cc_final: 0.7448 (mmp) REVERT: D 165 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8017 (mm-30) REVERT: F 27 ASP cc_start: 0.8623 (m-30) cc_final: 0.8302 (m-30) REVERT: F 60 GLN cc_start: 0.8396 (mt0) cc_final: 0.8083 (mt0) REVERT: G 22 LYS cc_start: 0.8894 (tptp) cc_final: 0.8671 (tptt) REVERT: G 42 ASP cc_start: 0.7584 (t0) cc_final: 0.7192 (t0) REVERT: H 59 SER cc_start: 0.8522 (m) cc_final: 0.7950 (p) REVERT: H 62 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8611 (mm) REVERT: I 52 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7534 (mt-10) outliers start: 36 outliers final: 26 residues processed: 262 average time/residue: 0.2208 time to fit residues: 76.3727 Evaluate side-chains 260 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 231 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 61 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8117 Z= 0.217 Angle : 0.688 11.772 10903 Z= 0.354 Chirality : 0.039 0.263 1185 Planarity : 0.004 0.052 1392 Dihedral : 5.007 42.296 1074 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.76 % Favored : 95.14 % Rotamer: Outliers : 4.12 % Allowed : 25.43 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 1.54 (0.26), residues: 967 helix: 1.84 (0.18), residues: 760 sheet: 0.08 (1.06), residues: 22 loop : -2.43 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 106 HIS 0.004 0.001 HIS I 66 PHE 0.038 0.001 PHE C 107 TYR 0.030 0.001 TYR C 151 ARG 0.003 0.000 ARG F 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 238 time to evaluate : 0.943 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 33 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7227 (tm-30) REVERT: A 45 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8362 (mmtm) REVERT: A 140 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7815 (tm-30) REVERT: B 39 MET cc_start: 0.4308 (mtm) cc_final: 0.3668 (tmm) REVERT: B 82 LYS cc_start: 0.8290 (mmpt) cc_final: 0.7965 (tptt) REVERT: C 153 PHE cc_start: 0.8891 (t80) cc_final: 0.8625 (m-80) REVERT: C 163 HIS cc_start: 0.8590 (OUTLIER) cc_final: 0.7920 (t70) REVERT: D 64 MET cc_start: 0.5629 (OUTLIER) cc_final: 0.5185 (tmm) REVERT: D 78 GLN cc_start: 0.8405 (tm-30) cc_final: 0.7841 (tm-30) REVERT: D 111 ASP cc_start: 0.7827 (t0) cc_final: 0.7215 (t0) REVERT: D 123 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8104 (tm-30) REVERT: D 155 MET cc_start: 0.7682 (mmt) cc_final: 0.7436 (mmp) REVERT: D 165 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8019 (mm-30) REVERT: F 27 ASP cc_start: 0.8640 (m-30) cc_final: 0.8280 (m-30) REVERT: F 60 GLN cc_start: 0.8457 (mt0) cc_final: 0.8098 (mt0) REVERT: G 22 LYS cc_start: 0.8941 (tptp) cc_final: 0.8701 (tptt) REVERT: G 42 ASP cc_start: 0.7610 (t0) cc_final: 0.7206 (t0) REVERT: H 59 SER cc_start: 0.8540 (m) cc_final: 0.7971 (p) REVERT: H 62 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8701 (mm) REVERT: I 7 LYS cc_start: 0.8868 (ptmm) cc_final: 0.8449 (tmmt) REVERT: I 52 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7542 (mt-10) outliers start: 36 outliers final: 28 residues processed: 255 average time/residue: 0.2137 time to fit residues: 71.3309 Evaluate side-chains 260 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 229 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 0.0970 chunk 80 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 GLN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 ASN J 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8117 Z= 0.203 Angle : 0.710 12.722 10903 Z= 0.361 Chirality : 0.040 0.229 1185 Planarity : 0.004 0.042 1392 Dihedral : 4.862 43.661 1073 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Rotamer: Outliers : 4.58 % Allowed : 24.74 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.10 % 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: 1.65 (0.26), residues: 967 helix: 1.93 (0.18), residues: 761 sheet: 0.12 (1.07), residues: 22 loop : -2.50 (0.39), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 106 HIS 0.004 0.001 HIS C 163 PHE 0.036 0.001 PHE C 107 TYR 0.038 0.001 TYR C 151 ARG 0.006 0.000 ARG I 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 240 time to evaluate : 0.934 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 140 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7843 (tm-30) REVERT: B 39 MET cc_start: 0.4349 (mtm) cc_final: 0.3682 (tmm) REVERT: B 67 THR cc_start: 0.8626 (m) cc_final: 0.8381 (p) REVERT: B 82 LYS cc_start: 0.8316 (mmpt) cc_final: 0.7982 (tptt) REVERT: C 151 TYR cc_start: 0.8200 (m-80) cc_final: 0.7920 (m-80) REVERT: C 153 PHE cc_start: 0.8844 (t80) cc_final: 0.8635 (m-80) REVERT: C 163 HIS cc_start: 0.8555 (OUTLIER) cc_final: 0.7904 (t70) REVERT: D 64 MET cc_start: 0.5507 (OUTLIER) cc_final: 0.5147 (tmm) REVERT: D 78 GLN cc_start: 0.8413 (tm-30) cc_final: 0.7844 (tm-30) REVERT: D 111 ASP cc_start: 0.7840 (t0) cc_final: 0.7283 (t0) REVERT: D 123 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8086 (tm-30) REVERT: D 155 MET cc_start: 0.7720 (mmt) cc_final: 0.7500 (mmp) REVERT: D 165 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7961 (mm-30) REVERT: F 27 ASP cc_start: 0.8594 (m-30) cc_final: 0.8293 (m-30) REVERT: F 60 GLN cc_start: 0.8428 (mt0) cc_final: 0.8069 (mt0) REVERT: G 22 LYS cc_start: 0.8959 (tptp) cc_final: 0.8724 (tptt) REVERT: G 42 ASP cc_start: 0.7588 (t0) cc_final: 0.7209 (t0) REVERT: H 59 SER cc_start: 0.8557 (m) cc_final: 0.8020 (p) REVERT: H 62 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8712 (mm) REVERT: H 79 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.7478 (m-40) REVERT: I 7 LYS cc_start: 0.8760 (ptmm) cc_final: 0.8356 (tptp) REVERT: I 52 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7326 (mt-10) outliers start: 40 outliers final: 27 residues processed: 261 average time/residue: 0.2340 time to fit residues: 80.0650 Evaluate side-chains 252 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 221 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 79 ASN Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.0170 chunk 77 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8117 Z= 0.213 Angle : 0.735 12.858 10903 Z= 0.373 Chirality : 0.042 0.316 1185 Planarity : 0.004 0.041 1392 Dihedral : 4.874 43.125 1073 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.44 % Allowed : 26.69 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.10 % 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: 1.61 (0.26), residues: 967 helix: 1.90 (0.18), residues: 760 sheet: 0.09 (1.06), residues: 22 loop : -2.49 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 106 HIS 0.005 0.001 HIS F 94 PHE 0.050 0.001 PHE C 107 TYR 0.031 0.001 TYR C 151 ARG 0.009 0.000 ARG I 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 225 time to evaluate : 1.037 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 33 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7151 (tm-30) REVERT: A 140 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 39 MET cc_start: 0.4372 (mtm) cc_final: 0.3731 (tmm) REVERT: B 67 THR cc_start: 0.8639 (m) cc_final: 0.8390 (p) REVERT: B 82 LYS cc_start: 0.8353 (mmpt) cc_final: 0.8128 (tptt) REVERT: C 151 TYR cc_start: 0.8217 (m-80) cc_final: 0.7901 (m-80) REVERT: C 163 HIS cc_start: 0.8558 (OUTLIER) cc_final: 0.7908 (t70) REVERT: D 64 MET cc_start: 0.5475 (OUTLIER) cc_final: 0.5159 (tmm) REVERT: D 78 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7860 (tm-30) REVERT: D 123 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8065 (tm-30) REVERT: D 155 MET cc_start: 0.7723 (mmt) cc_final: 0.7513 (mmp) REVERT: F 27 ASP cc_start: 0.8623 (m-30) cc_final: 0.8279 (m-30) REVERT: F 60 GLN cc_start: 0.8426 (mt0) cc_final: 0.8052 (mt0) REVERT: G 22 LYS cc_start: 0.8946 (tptp) cc_final: 0.8737 (tptt) REVERT: G 42 ASP cc_start: 0.7609 (t0) cc_final: 0.7218 (t0) REVERT: H 59 SER cc_start: 0.8608 (m) cc_final: 0.8102 (p) REVERT: H 62 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8596 (mm) REVERT: I 7 LYS cc_start: 0.8743 (ptmm) cc_final: 0.8355 (tptp) outliers start: 30 outliers final: 23 residues processed: 243 average time/residue: 0.2080 time to fit residues: 66.6376 Evaluate side-chains 246 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 220 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain J residue 32 MET Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 75 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 23 optimal weight: 0.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8117 Z= 0.207 Angle : 0.754 13.137 10903 Z= 0.379 Chirality : 0.041 0.216 1185 Planarity : 0.004 0.046 1392 Dihedral : 4.876 42.355 1073 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.98 % Allowed : 27.38 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.10 % 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: 1.66 (0.26), residues: 967 helix: 1.94 (0.18), residues: 764 sheet: 0.10 (1.06), residues: 22 loop : -2.56 (0.39), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 106 HIS 0.004 0.001 HIS C 163 PHE 0.018 0.001 PHE D 118 TYR 0.031 0.001 TYR C 151 ARG 0.008 0.000 ARG I 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 228 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7911 (tm-30) REVERT: B 39 MET cc_start: 0.4403 (mtm) cc_final: 0.3746 (tmm) REVERT: B 67 THR cc_start: 0.8623 (m) cc_final: 0.8378 (p) REVERT: B 82 LYS cc_start: 0.8259 (mmpt) cc_final: 0.7916 (tptt) REVERT: C 151 TYR cc_start: 0.8242 (m-80) cc_final: 0.7874 (m-80) REVERT: C 153 PHE cc_start: 0.8344 (m-80) cc_final: 0.8134 (m-80) REVERT: C 163 HIS cc_start: 0.8505 (OUTLIER) cc_final: 0.7881 (t70) REVERT: D 64 MET cc_start: 0.5343 (OUTLIER) cc_final: 0.5070 (tmm) REVERT: D 78 GLN cc_start: 0.8405 (tm-30) cc_final: 0.7853 (tm-30) REVERT: D 123 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8067 (tm-30) REVERT: D 155 MET cc_start: 0.7767 (mmt) cc_final: 0.7540 (mmp) REVERT: F 27 ASP cc_start: 0.8608 (m-30) cc_final: 0.8284 (m-30) REVERT: F 60 GLN cc_start: 0.8412 (mt0) cc_final: 0.8036 (mt0) REVERT: F 93 ARG cc_start: 0.8275 (mmp80) cc_final: 0.7893 (mmp80) REVERT: G 22 LYS cc_start: 0.8969 (tptp) cc_final: 0.8715 (tptt) REVERT: G 42 ASP cc_start: 0.7719 (t0) cc_final: 0.7311 (t0) REVERT: H 59 SER cc_start: 0.8650 (m) cc_final: 0.8150 (p) REVERT: H 62 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8621 (mm) REVERT: I 7 LYS cc_start: 0.8673 (ptmm) cc_final: 0.8319 (tptp) REVERT: I 51 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7581 (pptt) outliers start: 26 outliers final: 21 residues processed: 246 average time/residue: 0.2093 time to fit residues: 67.7282 Evaluate side-chains 243 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 219 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 149 CYS Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 55 CYS Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain I residue 35 CYS Chi-restraints excluded: chain J residue 44 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.0570 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN I 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.075381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.061817 restraints weight = 30021.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.063452 restraints weight = 16750.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.064573 restraints weight = 11246.909| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8117 Z= 0.215 Angle : 0.752 13.740 10903 Z= 0.377 Chirality : 0.041 0.215 1185 Planarity : 0.004 0.051 1392 Dihedral : 4.882 41.272 1073 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.21 % Allowed : 27.49 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.10 % 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: 1.72 (0.27), residues: 967 helix: 1.97 (0.18), residues: 763 sheet: 0.14 (1.06), residues: 22 loop : -2.49 (0.39), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 42 HIS 0.004 0.001 HIS C 163 PHE 0.031 0.001 PHE B 41 TYR 0.029 0.001 TYR C 151 ARG 0.006 0.000 ARG I 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2130.52 seconds wall clock time: 39 minutes 12.46 seconds (2352.46 seconds total)