Starting phenix.real_space_refine on Thu Feb 15 06:01:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqc_34023/02_2024/7yqc_34023.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqc_34023/02_2024/7yqc_34023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqc_34023/02_2024/7yqc_34023.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqc_34023/02_2024/7yqc_34023.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqc_34023/02_2024/7yqc_34023.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqc_34023/02_2024/7yqc_34023.pdb" } resolution = 2.82 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= 0.056 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 28 5.16 5 C 7287 2.51 5 N 1939 2.21 5 O 2142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "C ASP 28": "OD1" <-> "OD2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "D ASP 201": "OD1" <-> "OD2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "E ASP 28": "OD1" <-> "OD2" Residue "E GLU 160": "OE1" <-> "OE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E ASP 201": "OD1" <-> "OD2" Residue "E GLU 240": "OE1" <-> "OE2" Residue "F GLU 20": "OE1" <-> "OE2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 54": "OD1" <-> "OD2" Residue "F TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 208": "OE1" <-> "OE2" Residue "F GLU 240": "OE1" <-> "OE2" Residue "G ASP 28": "OD1" <-> "OD2" Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 54": "OD1" <-> "OD2" Residue "G GLU 169": "OE1" <-> "OE2" Residue "G TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11396 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1628 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1628 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1628 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1628 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1628 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1628 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1628 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 6.01, per 1000 atoms: 0.53 Number of scatterers: 11396 At special positions: 0 Unit cell: (110.24, 112.32, 79.04, 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 28 16.00 O 2142 8.00 N 1939 7.00 C 7287 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 - 3.50 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: 4.02 Conformation dependent library (CDL) restraints added in 2.0 seconds 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2744 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 0 sheets defined 85.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 8 through 45 removed outlier: 4.305A pdb=" N PHE A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 46 through 51 removed outlier: 6.514A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 142 removed outlier: 3.521A pdb=" N ILE A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 152 through 196 removed outlier: 3.515A pdb=" N LEU A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 238 removed outlier: 3.509A pdb=" N VAL A 206 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'B' and resid 8 through 32 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 54 through 59 removed outlier: 3.693A pdb=" N ILE B 58 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS B 59 " --> pdb=" O THR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 142 removed outlier: 3.587A pdb=" N ILE B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 152 through 196 removed outlier: 3.545A pdb=" N TYR B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 238 removed outlier: 3.531A pdb=" N VAL B 206 " --> pdb=" O TYR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'C' and resid 8 through 32 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.531A pdb=" N LEU C 50 " --> pdb=" O GLU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 59 Processing helix chain 'C' and resid 112 through 142 Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 152 through 196 removed outlier: 3.542A pdb=" N TYR C 183 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 238 removed outlier: 3.545A pdb=" N ARG C 204 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 206 " --> pdb=" O TYR C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 244 Processing helix chain 'D' and resid 8 through 32 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 54 through 58 Processing helix chain 'D' and resid 112 through 142 removed outlier: 3.540A pdb=" N ILE D 118 " --> pdb=" O GLN D 114 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Proline residue: D 124 - end of helix Processing helix chain 'D' and resid 152 through 196 removed outlier: 3.538A pdb=" N TYR D 183 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 238 removed outlier: 3.648A pdb=" N ARG D 204 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 206 " --> pdb=" O TYR D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 244 Processing helix chain 'E' and resid 8 through 45 removed outlier: 4.349A pdb=" N PHE E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) Proline residue: E 35 - end of helix Processing helix chain 'E' and resid 46 through 51 removed outlier: 6.566A pdb=" N ILE E 49 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 142 removed outlier: 3.507A pdb=" N ASP E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE E 118 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 152 through 196 removed outlier: 3.529A pdb=" N SER E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 238 removed outlier: 3.527A pdb=" N ARG E 204 " --> pdb=" O GLU E 200 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL E 206 " --> pdb=" O TYR E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 244 Processing helix chain 'F' and resid 8 through 32 Processing helix chain 'F' and resid 32 through 45 Processing helix chain 'F' and resid 46 through 51 removed outlier: 6.598A pdb=" N ILE F 49 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 59 removed outlier: 3.720A pdb=" N HIS F 59 " --> pdb=" O THR F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 142 removed outlier: 3.587A pdb=" N ILE F 118 " --> pdb=" O GLN F 114 " (cutoff:3.500A) Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 152 through 196 removed outlier: 3.505A pdb=" N TYR F 183 " --> pdb=" O ILE F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 238 removed outlier: 3.571A pdb=" N VAL F 206 " --> pdb=" O TYR F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 244 Processing helix chain 'G' and resid 8 through 32 Processing helix chain 'G' and resid 32 through 45 Processing helix chain 'G' and resid 46 through 51 removed outlier: 6.624A pdb=" N ILE G 49 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 142 removed outlier: 3.537A pdb=" N LYS G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Proline residue: G 124 - end of helix Processing helix chain 'G' and resid 152 through 196 removed outlier: 3.608A pdb=" N TYR G 183 " --> pdb=" O ILE G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 238 removed outlier: 3.547A pdb=" N VAL G 206 " --> pdb=" O TYR G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 244 932 hydrogen bonds defined for protein. 2733 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: 3.25 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1946 1.31 - 1.43: 2639 1.43 - 1.56: 6916 1.56 - 1.68: 0 1.68 - 1.81: 49 Bond restraints: 11550 Sorted by residual: bond pdb=" C PRO F 35 " pdb=" O PRO F 35 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.26e-02 6.30e+03 2.08e+01 bond pdb=" C PRO E 35 " pdb=" O PRO E 35 " ideal model delta sigma weight residual 1.237 1.184 0.053 1.26e-02 6.30e+03 1.76e+01 bond pdb=" CA ALA B 26 " pdb=" CB ALA B 26 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.56e-02 4.11e+03 1.55e+01 bond pdb=" CA ALA D 26 " pdb=" CB ALA D 26 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.56e-02 4.11e+03 1.53e+01 bond pdb=" C PRO E 245 " pdb=" O PRO E 245 " ideal model delta sigma weight residual 1.237 1.188 0.049 1.26e-02 6.30e+03 1.53e+01 ... (remaining 11545 not shown) Histogram of bond angle deviations from ideal: 97.58 - 104.88: 178 104.88 - 112.17: 5012 112.17 - 119.46: 5784 119.46 - 126.76: 4543 126.76 - 134.05: 51 Bond angle restraints: 15568 Sorted by residual: angle pdb=" N LYS C 110 " pdb=" CA LYS C 110 " pdb=" C LYS C 110 " ideal model delta sigma weight residual 110.43 120.87 -10.44 1.31e+00 5.83e-01 6.35e+01 angle pdb=" N LYS B 110 " pdb=" CA LYS B 110 " pdb=" C LYS B 110 " ideal model delta sigma weight residual 110.35 120.77 -10.42 1.36e+00 5.41e-01 5.88e+01 angle pdb=" N LYS G 110 " pdb=" CA LYS G 110 " pdb=" C LYS G 110 " ideal model delta sigma weight residual 110.35 120.71 -10.36 1.36e+00 5.41e-01 5.81e+01 angle pdb=" N LYS A 110 " pdb=" CA LYS A 110 " pdb=" C LYS A 110 " ideal model delta sigma weight residual 110.35 120.49 -10.14 1.36e+00 5.41e-01 5.56e+01 angle pdb=" N LYS F 110 " pdb=" CA LYS F 110 " pdb=" C LYS F 110 " ideal model delta sigma weight residual 110.35 119.95 -9.60 1.36e+00 5.41e-01 4.98e+01 ... (remaining 15563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 6258 17.28 - 34.56: 733 34.56 - 51.84: 210 51.84 - 69.12: 67 69.12 - 86.40: 5 Dihedral angle restraints: 7273 sinusoidal: 3108 harmonic: 4165 Sorted by residual: dihedral pdb=" C THR G 135 " pdb=" N THR G 135 " pdb=" CA THR G 135 " pdb=" CB THR G 135 " ideal model delta harmonic sigma weight residual -122.00 -136.46 14.46 0 2.50e+00 1.60e-01 3.34e+01 dihedral pdb=" C THR F 135 " pdb=" N THR F 135 " pdb=" CA THR F 135 " pdb=" CB THR F 135 " ideal model delta harmonic sigma weight residual -122.00 -135.76 13.76 0 2.50e+00 1.60e-01 3.03e+01 dihedral pdb=" C LEU A 109 " pdb=" N LEU A 109 " pdb=" CA LEU A 109 " pdb=" CB LEU A 109 " ideal model delta harmonic sigma weight residual -122.60 -135.76 13.16 0 2.50e+00 1.60e-01 2.77e+01 ... (remaining 7270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1073 0.106 - 0.212: 620 0.212 - 0.317: 124 0.317 - 0.423: 18 0.423 - 0.529: 13 Chirality restraints: 1848 Sorted by residual: chirality pdb=" CA LEU A 109 " pdb=" N LEU A 109 " pdb=" C LEU A 109 " pdb=" CB LEU A 109 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" CA LEU G 109 " pdb=" N LEU G 109 " pdb=" C LEU G 109 " pdb=" CB LEU G 109 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" CA LEU E 109 " pdb=" N LEU E 109 " pdb=" C LEU E 109 " pdb=" CB LEU E 109 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.94e+00 ... (remaining 1845 not shown) Planarity restraints: 1953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 241 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LYS D 241 " 0.058 2.00e-02 2.50e+03 pdb=" O LYS D 241 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE D 242 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 241 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.63e+00 pdb=" C LYS E 241 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS E 241 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE E 242 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 241 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" C LYS A 241 " 0.051 2.00e-02 2.50e+03 pdb=" O LYS A 241 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE A 242 " -0.017 2.00e-02 2.50e+03 ... (remaining 1950 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 4801 2.98 - 3.46: 11707 3.46 - 3.94: 19805 3.94 - 4.42: 22196 4.42 - 4.90: 36558 Nonbonded interactions: 95067 Sorted by model distance: nonbonded pdb=" O ASP D 201 " pdb=" OG1 THR D 205 " model vdw 2.497 2.440 nonbonded pdb=" O PHE D 153 " pdb=" OG SER D 156 " model vdw 2.503 2.440 nonbonded pdb=" O PHE G 153 " pdb=" OG SER G 156 " model vdw 2.505 2.440 nonbonded pdb=" C SER B 24 " pdb=" OG SER B 24 " model vdw 2.505 2.616 nonbonded pdb=" O PHE E 153 " pdb=" OG SER E 156 " model vdw 2.516 2.440 ... (remaining 95062 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.770 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: 3.580 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 30.910 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 : 0.013 0.061 11550 Z= 0.870 Angle : 1.865 11.277 15568 Z= 1.424 Chirality : 0.128 0.529 1848 Planarity : 0.007 0.033 1953 Dihedral : 16.597 86.404 4529 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 9.34 % Allowed : 9.81 % Favored : 80.85 % Cbeta Deviations : 1.75 % 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: 3.07 (0.18), residues: 1358 helix: 2.74 (0.13), residues: 1015 sheet: None (None), residues: 0 loop : -0.19 (0.26), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP F 139 HIS 0.009 0.003 HIS D 232 PHE 0.020 0.003 PHE C 33 TYR 0.021 0.003 TYR B 228 ARG 0.005 0.001 ARG F 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 132 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: A 169 GLU cc_start: 0.7543 (tt0) cc_final: 0.7322 (tt0) REVERT: A 178 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7156 (pt0) REVERT: A 240 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7309 (mp0) REVERT: B 149 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6303 (m-30) REVERT: B 223 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7126 (mm-30) REVERT: B 234 MET cc_start: 0.7337 (tmt) cc_final: 0.7071 (tmm) REVERT: B 240 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7248 (tp30) REVERT: C 38 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7989 (tp) REVERT: C 54 ASP cc_start: 0.7958 (t0) cc_final: 0.7758 (t0) REVERT: C 56 THR cc_start: 0.8805 (m) cc_final: 0.8463 (p) REVERT: D 5 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6701 (mt) REVERT: D 56 THR cc_start: 0.8911 (m) cc_final: 0.8695 (p) REVERT: D 109 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7219 (mm) REVERT: D 178 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.6856 (pt0) REVERT: D 204 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7904 (mmt90) REVERT: E 37 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7970 (tptt) REVERT: E 164 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.7012 (tp30) REVERT: F 5 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.5836 (pp) REVERT: F 38 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8115 (tp) REVERT: G 5 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6489 (mt) REVERT: G 178 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7523 (pt0) REVERT: G 234 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7213 (ttm) outliers start: 121 outliers final: 50 residues processed: 232 average time/residue: 1.3116 time to fit residues: 327.2337 Evaluate side-chains 177 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 113 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 124 PRO Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 204 ARG Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 37 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 124 PRO Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 124 PRO Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 104 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN B 134 ASN B 178 GLN C 134 ASN C 178 GLN D 178 GLN D 198 HIS E 134 ASN E 178 GLN F 134 ASN F 178 GLN G 134 ASN G 178 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11550 Z= 0.183 Angle : 0.505 10.280 15568 Z= 0.277 Chirality : 0.038 0.136 1848 Planarity : 0.003 0.032 1953 Dihedral : 10.327 59.911 1650 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 6.56 % Allowed : 13.59 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.95 (0.21), residues: 1358 helix: 3.20 (0.14), residues: 1085 sheet: None (None), residues: 0 loop : 0.04 (0.32), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 139 HIS 0.004 0.001 HIS E 198 PHE 0.007 0.001 PHE C 33 TYR 0.010 0.001 TYR B 228 ARG 0.004 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 136 time to evaluate : 1.428 Fit side-chains REVERT: A 49 ILE cc_start: 0.8405 (tt) cc_final: 0.8184 (tt) REVERT: A 55 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8271 (mp) REVERT: A 138 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7374 (ttm) REVERT: A 240 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7069 (mp0) REVERT: B 55 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8158 (mp) REVERT: B 223 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6983 (mm-30) REVERT: B 240 GLU cc_start: 0.7483 (tm-30) cc_final: 0.6907 (mp0) REVERT: C 38 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7761 (tp) REVERT: D 138 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.6919 (tpp) REVERT: D 240 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6852 (mp0) REVERT: E 58 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.8016 (pp) REVERT: E 138 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7640 (ttm) REVERT: E 164 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6900 (tp30) REVERT: E 240 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: F 5 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.5964 (pp) REVERT: F 38 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7899 (tp) REVERT: F 138 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7506 (ttm) REVERT: F 240 GLU cc_start: 0.7667 (tm-30) cc_final: 0.6826 (mp0) REVERT: G 16 ASP cc_start: 0.7634 (m-30) cc_final: 0.7416 (m-30) REVERT: G 28 ASP cc_start: 0.7813 (t70) cc_final: 0.7492 (t0) REVERT: G 42 ASP cc_start: 0.8317 (t0) cc_final: 0.8116 (t70) REVERT: G 49 ILE cc_start: 0.8634 (tt) cc_final: 0.8401 (tt) REVERT: G 138 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7496 (ttm) REVERT: G 178 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7437 (pt0) outliers start: 85 outliers final: 28 residues processed: 203 average time/residue: 1.2505 time to fit residues: 274.1606 Evaluate side-chains 159 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 117 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 178 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 134 ASN C 178 GLN C 198 HIS D 178 GLN E 178 GLN F 141 GLN F 178 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11550 Z= 0.242 Angle : 0.481 5.060 15568 Z= 0.264 Chirality : 0.039 0.120 1848 Planarity : 0.003 0.025 1953 Dihedral : 7.796 58.668 1561 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 6.72 % Allowed : 14.83 % Favored : 78.46 % 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: 3.59 (0.21), residues: 1358 helix: 2.93 (0.15), residues: 1085 sheet: None (None), residues: 0 loop : -0.04 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 139 HIS 0.005 0.001 HIS E 232 PHE 0.009 0.001 PHE F 44 TYR 0.008 0.001 TYR B 228 ARG 0.003 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 162 time to evaluate : 1.234 Fit side-chains REVERT: A 49 ILE cc_start: 0.8434 (tt) cc_final: 0.8233 (tt) REVERT: A 149 ASP cc_start: 0.6499 (OUTLIER) cc_final: 0.6006 (m-30) REVERT: A 223 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7145 (mm-30) REVERT: A 240 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: B 55 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8171 (mp) REVERT: B 178 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7289 (pt0) REVERT: B 234 MET cc_start: 0.7398 (tmt) cc_final: 0.6965 (tmm) REVERT: B 240 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: C 38 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7929 (tp) REVERT: C 109 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6838 (mm) REVERT: D 109 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6868 (mm) REVERT: E 28 ASP cc_start: 0.7877 (t70) cc_final: 0.7400 (t0) REVERT: E 58 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.8005 (pp) REVERT: E 138 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7612 (ttm) REVERT: E 164 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6977 (tp30) REVERT: E 219 LEU cc_start: 0.8128 (tp) cc_final: 0.7896 (tt) REVERT: E 240 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: F 6 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6090 (mttt) REVERT: F 38 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7972 (tp) REVERT: F 138 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7533 (ttm) REVERT: F 240 GLU cc_start: 0.7631 (tm-30) cc_final: 0.6879 (mp0) REVERT: G 16 ASP cc_start: 0.7634 (m-30) cc_final: 0.7285 (m-30) REVERT: G 28 ASP cc_start: 0.7906 (t70) cc_final: 0.7540 (t0) REVERT: G 138 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7468 (ttm) REVERT: G 178 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7513 (pt0) REVERT: G 234 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7044 (ttt) outliers start: 87 outliers final: 30 residues processed: 212 average time/residue: 1.1922 time to fit residues: 273.4436 Evaluate side-chains 193 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 145 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 241 LYS Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 0.0670 chunk 81 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 178 GLN C 178 GLN D 178 GLN E 178 GLN E 198 HIS F 141 GLN F 178 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11550 Z= 0.159 Angle : 0.425 6.598 15568 Z= 0.230 Chirality : 0.037 0.122 1848 Planarity : 0.003 0.024 1953 Dihedral : 6.706 56.328 1548 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 5.48 % Allowed : 16.37 % Favored : 78.15 % 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: 3.66 (0.22), residues: 1358 helix: 2.98 (0.15), residues: 1099 sheet: None (None), residues: 0 loop : -0.24 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 139 HIS 0.004 0.001 HIS E 232 PHE 0.006 0.001 PHE F 44 TYR 0.005 0.001 TYR G 228 ARG 0.005 0.000 ARG C 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 152 time to evaluate : 1.318 Fit side-chains REVERT: A 49 ILE cc_start: 0.8431 (tt) cc_final: 0.8221 (tt) REVERT: A 58 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8086 (pp) REVERT: A 181 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7491 (ttm-80) REVERT: A 223 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7181 (mm-30) REVERT: A 233 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7944 (t70) REVERT: A 240 GLU cc_start: 0.7620 (tm-30) cc_final: 0.6940 (mp0) REVERT: B 178 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7247 (pt0) REVERT: B 234 MET cc_start: 0.7510 (tmt) cc_final: 0.7070 (tmm) REVERT: B 240 GLU cc_start: 0.7531 (tm-30) cc_final: 0.6876 (mp0) REVERT: C 38 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7859 (tp) REVERT: C 109 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6450 (mm) REVERT: C 181 ARG cc_start: 0.7557 (mtm-85) cc_final: 0.7327 (ttp-110) REVERT: C 223 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7117 (tp30) REVERT: E 58 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.8003 (pp) REVERT: E 160 GLU cc_start: 0.6741 (mt-10) cc_final: 0.6453 (mt-10) REVERT: E 181 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7456 (ttm-80) REVERT: E 219 LEU cc_start: 0.8155 (tp) cc_final: 0.7911 (tt) REVERT: E 240 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: F 5 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6577 (pt) REVERT: F 38 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7937 (tp) REVERT: F 138 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7178 (tpp) REVERT: F 240 GLU cc_start: 0.7622 (tm-30) cc_final: 0.6937 (mp0) REVERT: G 16 ASP cc_start: 0.7647 (m-30) cc_final: 0.7284 (m-30) REVERT: G 28 ASP cc_start: 0.7923 (t70) cc_final: 0.7500 (t0) REVERT: G 138 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7004 (tpp) REVERT: G 178 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7479 (pt0) REVERT: G 234 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7043 (ttt) outliers start: 71 outliers final: 23 residues processed: 196 average time/residue: 1.1936 time to fit residues: 254.2078 Evaluate side-chains 170 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 133 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 181 ARG Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 chunk 53 optimal weight: 0.0770 chunk 109 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN C 178 GLN D 178 GLN E 178 GLN F 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11550 Z= 0.148 Angle : 0.410 6.436 15568 Z= 0.220 Chirality : 0.037 0.119 1848 Planarity : 0.003 0.022 1953 Dihedral : 5.500 54.892 1536 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 4.63 % Allowed : 17.37 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.22), residues: 1358 helix: 3.03 (0.15), residues: 1099 sheet: None (None), residues: 0 loop : -0.23 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 139 HIS 0.002 0.001 HIS G 198 PHE 0.004 0.001 PHE E 33 TYR 0.005 0.001 TYR G 228 ARG 0.003 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 139 time to evaluate : 1.400 Fit side-chains REVERT: A 49 ILE cc_start: 0.8479 (tt) cc_final: 0.8253 (tt) REVERT: A 58 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8066 (pp) REVERT: A 223 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7094 (mm-30) REVERT: A 240 GLU cc_start: 0.7632 (tm-30) cc_final: 0.6927 (mp0) REVERT: B 178 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7206 (pt0) REVERT: B 223 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7068 (mm-30) REVERT: B 234 MET cc_start: 0.7486 (tmt) cc_final: 0.7043 (tmm) REVERT: B 240 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: C 37 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8102 (mmtm) REVERT: C 38 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7882 (tp) REVERT: C 109 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6555 (mm) REVERT: C 223 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7147 (tp30) REVERT: E 135 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7813 (m) REVERT: E 160 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6441 (mt-10) REVERT: E 219 LEU cc_start: 0.8159 (tp) cc_final: 0.7911 (tt) REVERT: E 240 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: F 6 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6342 (mttt) REVERT: F 38 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7953 (tp) REVERT: F 138 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7165 (tpp) REVERT: F 240 GLU cc_start: 0.7636 (tm-30) cc_final: 0.6932 (mp0) REVERT: G 16 ASP cc_start: 0.7662 (m-30) cc_final: 0.7282 (m-30) REVERT: G 28 ASP cc_start: 0.7953 (t70) cc_final: 0.7532 (t0) REVERT: G 138 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7425 (tpp) REVERT: G 178 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7369 (pt0) REVERT: G 234 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.7033 (ttt) outliers start: 60 outliers final: 23 residues processed: 175 average time/residue: 1.2171 time to fit residues: 230.7928 Evaluate side-chains 167 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN E 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11550 Z= 0.307 Angle : 0.489 6.547 15568 Z= 0.264 Chirality : 0.040 0.123 1848 Planarity : 0.003 0.027 1953 Dihedral : 5.848 53.435 1536 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 5.41 % Allowed : 16.06 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.21), residues: 1358 helix: 2.79 (0.15), residues: 1085 sheet: None (None), residues: 0 loop : -0.17 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 139 HIS 0.005 0.002 HIS C 232 PHE 0.009 0.001 PHE A 44 TYR 0.005 0.001 TYR B 228 ARG 0.004 0.000 ARG F 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 164 time to evaluate : 1.454 Fit side-chains REVERT: A 49 ILE cc_start: 0.8567 (tt) cc_final: 0.8333 (tt) REVERT: A 58 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8111 (pp) REVERT: A 138 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7170 (tmm) REVERT: A 223 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7182 (mm-30) REVERT: A 240 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: B 160 GLU cc_start: 0.6749 (mt-10) cc_final: 0.6534 (mt-10) REVERT: B 164 GLU cc_start: 0.6733 (tt0) cc_final: 0.6431 (tp30) REVERT: B 178 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7322 (pt0) REVERT: B 223 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7104 (mm-30) REVERT: B 234 MET cc_start: 0.7478 (tmt) cc_final: 0.6987 (tmm) REVERT: B 240 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: C 37 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8059 (mmtm) REVERT: C 38 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7915 (tp) REVERT: D 109 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6551 (mm) REVERT: E 28 ASP cc_start: 0.7950 (t70) cc_final: 0.7498 (t0) REVERT: E 138 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7159 (tmm) REVERT: E 160 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6657 (mt-10) REVERT: E 219 LEU cc_start: 0.8175 (tp) cc_final: 0.7929 (tt) REVERT: E 236 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8248 (mm) REVERT: E 240 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: F 6 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6321 (mttt) REVERT: F 37 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7902 (mptp) REVERT: F 38 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7951 (tp) REVERT: F 138 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7492 (ttm) REVERT: F 240 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: G 16 ASP cc_start: 0.7702 (m-30) cc_final: 0.7306 (m-30) REVERT: G 28 ASP cc_start: 0.7922 (t70) cc_final: 0.7537 (t0) REVERT: G 138 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7488 (ttm) REVERT: G 159 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: G 178 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: G 234 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.7009 (ttt) REVERT: G 240 GLU cc_start: 0.6884 (mp0) cc_final: 0.6586 (mp0) outliers start: 70 outliers final: 29 residues processed: 204 average time/residue: 1.2557 time to fit residues: 276.3122 Evaluate side-chains 199 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 150 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 240 GLU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 93 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 178 GLN F 141 GLN F 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11550 Z= 0.196 Angle : 0.435 6.568 15568 Z= 0.236 Chirality : 0.038 0.117 1848 Planarity : 0.003 0.025 1953 Dihedral : 5.639 53.587 1536 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 4.63 % Allowed : 17.30 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.50 (0.22), residues: 1358 helix: 2.89 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : -0.27 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 139 HIS 0.003 0.001 HIS C 232 PHE 0.004 0.001 PHE E 33 TYR 0.005 0.001 TYR B 202 ARG 0.005 0.000 ARG F 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 129 time to evaluate : 1.259 Fit side-chains REVERT: A 49 ILE cc_start: 0.8570 (tt) cc_final: 0.8340 (tt) REVERT: A 58 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8055 (pp) REVERT: A 223 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7166 (mm-30) REVERT: A 240 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: B 178 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7292 (pt0) REVERT: B 223 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7078 (mm-30) REVERT: B 234 MET cc_start: 0.7467 (tmt) cc_final: 0.7024 (tmm) REVERT: B 240 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: C 37 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8103 (mmtm) REVERT: C 38 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7907 (tp) REVERT: D 109 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6383 (mm) REVERT: E 181 ARG cc_start: 0.7667 (ttm-80) cc_final: 0.7306 (ttp-110) REVERT: E 219 LEU cc_start: 0.8191 (tp) cc_final: 0.7926 (tt) REVERT: E 240 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: F 37 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8302 (mmtm) REVERT: F 38 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7951 (tp) REVERT: F 149 ASP cc_start: 0.6654 (OUTLIER) cc_final: 0.6267 (m-30) REVERT: F 159 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7151 (mp0) REVERT: F 240 GLU cc_start: 0.7553 (tm-30) cc_final: 0.6868 (mp0) REVERT: G 16 ASP cc_start: 0.7684 (m-30) cc_final: 0.7287 (m-30) REVERT: G 28 ASP cc_start: 0.7940 (t70) cc_final: 0.7536 (t0) REVERT: G 138 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7492 (tpp) REVERT: G 159 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: G 212 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8077 (ttmt) REVERT: G 234 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.7046 (ttt) outliers start: 60 outliers final: 28 residues processed: 169 average time/residue: 1.2943 time to fit residues: 236.0630 Evaluate side-chains 170 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 127 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 178 GLN F 141 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11550 Z= 0.228 Angle : 0.450 6.506 15568 Z= 0.244 Chirality : 0.038 0.115 1848 Planarity : 0.003 0.023 1953 Dihedral : 5.202 53.539 1527 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 4.25 % Allowed : 17.92 % Favored : 77.84 % 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: 3.10 (0.22), residues: 1358 helix: 2.51 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -0.42 (0.35), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 139 HIS 0.004 0.001 HIS G 198 PHE 0.005 0.001 PHE D 153 TYR 0.004 0.001 TYR B 228 ARG 0.004 0.000 ARG F 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 135 time to evaluate : 1.513 Fit side-chains REVERT: A 49 ILE cc_start: 0.8588 (tt) cc_final: 0.8358 (tt) REVERT: A 58 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8094 (pp) REVERT: A 223 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7157 (mm-30) REVERT: A 234 MET cc_start: 0.7533 (ttp) cc_final: 0.7063 (ttt) REVERT: A 240 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: B 160 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6467 (mt-10) REVERT: B 178 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: B 223 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7090 (mm-30) REVERT: B 234 MET cc_start: 0.7468 (tmt) cc_final: 0.7025 (tmm) REVERT: B 240 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: C 37 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8087 (mmtm) REVERT: C 38 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7912 (tp) REVERT: D 109 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6542 (mm) REVERT: E 159 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6983 (mp0) REVERT: E 181 ARG cc_start: 0.7660 (ttm-80) cc_final: 0.7284 (ttp-110) REVERT: E 219 LEU cc_start: 0.8179 (tp) cc_final: 0.7920 (tt) REVERT: E 240 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: F 6 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6263 (mttt) REVERT: F 37 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7974 (mptp) REVERT: F 38 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7959 (tp) REVERT: F 138 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7160 (tpp) REVERT: F 159 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7100 (mp0) REVERT: F 240 GLU cc_start: 0.7563 (tm-30) cc_final: 0.6876 (mp0) REVERT: G 16 ASP cc_start: 0.7692 (m-30) cc_final: 0.7288 (m-30) REVERT: G 28 ASP cc_start: 0.7958 (t70) cc_final: 0.7541 (t0) REVERT: G 138 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7485 (tpp) REVERT: G 159 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7300 (mt-10) REVERT: G 212 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8087 (ttmt) REVERT: G 234 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.7029 (ttt) outliers start: 55 outliers final: 27 residues processed: 170 average time/residue: 1.3724 time to fit residues: 250.6863 Evaluate side-chains 172 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 129 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 178 GLN F 141 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11550 Z= 0.183 Angle : 0.428 6.535 15568 Z= 0.233 Chirality : 0.037 0.121 1848 Planarity : 0.003 0.023 1953 Dihedral : 4.880 54.232 1525 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 4.09 % Allowed : 18.30 % Favored : 77.61 % 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: 3.48 (0.22), residues: 1358 helix: 2.86 (0.15), residues: 1099 sheet: None (None), residues: 0 loop : -0.34 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 139 HIS 0.003 0.001 HIS G 198 PHE 0.004 0.001 PHE E 33 TYR 0.005 0.001 TYR B 202 ARG 0.005 0.000 ARG F 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 129 time to evaluate : 1.222 Fit side-chains REVERT: A 49 ILE cc_start: 0.8574 (tt) cc_final: 0.8356 (tt) REVERT: A 58 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8053 (pp) REVERT: A 223 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7159 (mm-30) REVERT: A 240 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: B 110 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7928 (mmmm) REVERT: B 160 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6487 (mt-10) REVERT: B 178 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7279 (pt0) REVERT: B 223 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7104 (mm-30) REVERT: B 234 MET cc_start: 0.7462 (tmt) cc_final: 0.7023 (tmm) REVERT: B 240 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: C 37 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8109 (mmtm) REVERT: C 38 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7929 (tp) REVERT: D 109 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6453 (mm) REVERT: D 181 ARG cc_start: 0.7900 (ttp-110) cc_final: 0.7602 (ttm110) REVERT: E 181 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7300 (ttp-110) REVERT: E 219 LEU cc_start: 0.8192 (tp) cc_final: 0.7927 (tt) REVERT: E 240 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: F 6 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6150 (mttt) REVERT: F 37 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8306 (mmtm) REVERT: F 38 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7942 (tp) REVERT: F 138 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7124 (tpp) REVERT: F 240 GLU cc_start: 0.7593 (tm-30) cc_final: 0.6932 (mp0) REVERT: G 16 ASP cc_start: 0.7708 (m-30) cc_final: 0.7301 (m-30) REVERT: G 28 ASP cc_start: 0.7971 (t70) cc_final: 0.7547 (t0) REVERT: G 138 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7441 (tpp) REVERT: G 159 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7218 (mt-10) REVERT: G 160 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6713 (mt-10) REVERT: G 234 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7033 (ttt) outliers start: 53 outliers final: 30 residues processed: 161 average time/residue: 1.2765 time to fit residues: 221.9081 Evaluate side-chains 172 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 127 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 0.0170 chunk 121 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 10 optimal weight: 0.0470 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN D 178 GLN F 141 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11550 Z= 0.153 Angle : 0.412 6.428 15568 Z= 0.222 Chirality : 0.037 0.119 1848 Planarity : 0.003 0.025 1953 Dihedral : 4.644 50.836 1525 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.55 % Allowed : 18.76 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.22), residues: 1358 helix: 2.97 (0.15), residues: 1106 sheet: None (None), residues: 0 loop : -0.24 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 139 HIS 0.002 0.001 HIS G 198 PHE 0.005 0.001 PHE F 44 TYR 0.005 0.001 TYR B 228 ARG 0.005 0.000 ARG F 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 131 time to evaluate : 1.450 Fit side-chains REVERT: A 49 ILE cc_start: 0.8545 (tt) cc_final: 0.8340 (tt) REVERT: A 58 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8079 (pp) REVERT: A 159 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7137 (mp0) REVERT: A 178 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7312 (pt0) REVERT: A 223 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7059 (mm-30) REVERT: A 240 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: B 160 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6437 (mt-10) REVERT: B 178 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7217 (pt0) REVERT: B 223 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7100 (mm-30) REVERT: B 234 MET cc_start: 0.7454 (tmt) cc_final: 0.7018 (tmm) REVERT: B 240 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: C 37 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8105 (mmtm) REVERT: C 38 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7877 (tp) REVERT: C 181 ARG cc_start: 0.7698 (ttp-110) cc_final: 0.7358 (ttm110) REVERT: D 178 GLN cc_start: 0.7618 (pt0) cc_final: 0.7216 (pt0) REVERT: E 135 THR cc_start: 0.8014 (t) cc_final: 0.7770 (m) REVERT: E 138 MET cc_start: 0.8120 (tmm) cc_final: 0.7852 (tmm) REVERT: E 181 ARG cc_start: 0.7544 (ttm-80) cc_final: 0.7218 (ttp-110) REVERT: E 240 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: F 6 LYS cc_start: 0.6744 (OUTLIER) cc_final: 0.6156 (mttt) REVERT: F 38 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7942 (tp) REVERT: F 138 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7092 (tpp) REVERT: F 240 GLU cc_start: 0.7601 (tm-30) cc_final: 0.6906 (mp0) REVERT: G 16 ASP cc_start: 0.7701 (m-30) cc_final: 0.7293 (m-30) REVERT: G 28 ASP cc_start: 0.7999 (t70) cc_final: 0.7567 (t0) REVERT: G 138 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7433 (tpp) REVERT: G 212 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8088 (ttmt) REVERT: G 234 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7098 (ttt) REVERT: G 240 GLU cc_start: 0.6824 (mp0) cc_final: 0.6562 (mp0) outliers start: 46 outliers final: 23 residues processed: 155 average time/residue: 1.3165 time to fit residues: 219.8890 Evaluate side-chains 160 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 233 ASP Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain G residue 234 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.129125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.109573 restraints weight = 12147.593| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.70 r_work: 0.2953 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11550 Z= 0.180 Angle : 0.743 59.182 15568 Z= 0.438 Chirality : 0.041 0.735 1848 Planarity : 0.003 0.029 1953 Dihedral : 4.611 50.847 1520 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.93 % Allowed : 19.46 % Favored : 77.61 % Cbeta Deviations : 0.07 % 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: 3.64 (0.22), residues: 1358 helix: 2.95 (0.15), residues: 1106 sheet: None (None), residues: 0 loop : -0.24 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 139 HIS 0.002 0.001 HIS G 198 PHE 0.004 0.001 PHE F 44 TYR 0.005 0.001 TYR B 228 ARG 0.005 0.000 ARG F 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4234.04 seconds wall clock time: 75 minutes 53.85 seconds (4553.85 seconds total)