Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 04:08:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqc_34023/04_2023/7yqc_34023.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqc_34023/04_2023/7yqc_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_34023/04_2023/7yqc_34023.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqc_34023/04_2023/7yqc_34023.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqc_34023/04_2023/7yqc_34023.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqc_34023/04_2023/7yqc_34023.pdb" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 6.18, per 1000 atoms: 0.54 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: 4.42 Conformation dependent library (CDL) restraints added in 1.6 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: 0.29 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: 3.07 Time building geometry restraints manager: 4.77 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: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 4.120 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 30.480 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 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:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.130 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.333 Fit side-chains revert: symmetry clash outliers start: 121 outliers final: 50 residues processed: 232 average time/residue: 1.3409 time to fit residues: 334.4585 Evaluate side-chains 162 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 112 time to evaluate : 1.533 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 46 residues processed: 4 average time/residue: 0.3810 time to fit residues: 3.9613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 104 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 0.7592 moved from start: 0.2099 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= 0.189 Angle : 0.508 10.234 15568 Z= 0.279 Chirality : 0.039 0.137 1848 Planarity : 0.004 0.036 1953 Dihedral : 3.775 24.621 1505 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer Outliers : 7.10 % 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: 3.90 (0.21), residues: 1358 helix: 3.16 (0.14), residues: 1085 sheet: None (None), residues: 0 loop : 0.04 (0.32), residues: 273 *********************** 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 229 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 137 time to evaluate : 1.424 Fit side-chains outliers start: 92 outliers final: 41 residues processed: 211 average time/residue: 1.2970 time to fit residues: 295.1316 Evaluate side-chains 160 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 119 time to evaluate : 1.434 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 38 residues processed: 3 average time/residue: 0.8108 time to fit residues: 4.7674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 100 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 134 ASN C 178 GLN D 178 GLN E 178 GLN F 141 GLN F 178 GLN G 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 11550 Z= 0.296 Angle : 0.511 5.875 15568 Z= 0.280 Chirality : 0.041 0.121 1848 Planarity : 0.003 0.026 1953 Dihedral : 3.838 26.453 1505 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 7.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.44 (0.21), residues: 1358 helix: 2.81 (0.15), residues: 1085 sheet: None (None), residues: 0 loop : -0.04 (0.34), residues: 273 *********************** 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 262 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 168 time to evaluate : 1.492 Fit side-chains outliers start: 94 outliers final: 49 residues processed: 227 average time/residue: 1.2867 time to fit residues: 315.5467 Evaluate side-chains 209 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 160 time to evaluate : 1.380 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 38 residues processed: 11 average time/residue: 0.2698 time to fit residues: 5.9953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN B 178 GLN C 178 GLN D 178 GLN E 178 GLN E 198 HIS F 134 ASN F 141 GLN F 178 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2896 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= 0.163 Angle : 0.428 5.017 15568 Z= 0.233 Chirality : 0.037 0.120 1848 Planarity : 0.003 0.026 1953 Dihedral : 3.523 21.712 1505 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 7.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.22), residues: 1358 helix: 3.06 (0.15), residues: 1085 sheet: None (None), residues: 0 loop : -0.12 (0.34), residues: 273 *********************** 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 241 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 150 time to evaluate : 1.534 Fit side-chains outliers start: 91 outliers final: 48 residues processed: 209 average time/residue: 1.2451 time to fit residues: 281.5158 Evaluate side-chains 175 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 127 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 38 residues processed: 11 average time/residue: 0.2309 time to fit residues: 5.5196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 178 GLN E 178 GLN F 141 GLN F 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11550 Z= 0.174 Angle : 0.435 7.158 15568 Z= 0.233 Chirality : 0.037 0.119 1848 Planarity : 0.003 0.024 1953 Dihedral : 3.476 20.912 1505 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 5.87 % 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: 3.01 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : -0.26 (0.35), residues: 266 *********************** 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 210 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 134 time to evaluate : 1.352 Fit side-chains outliers start: 76 outliers final: 44 residues processed: 188 average time/residue: 1.3385 time to fit residues: 271.9260 Evaluate side-chains 169 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 125 time to evaluate : 1.525 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 35 residues processed: 9 average time/residue: 0.1642 time to fit residues: 4.3633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 11550 Z= 0.217 Angle : 0.449 7.248 15568 Z= 0.241 Chirality : 0.038 0.117 1848 Planarity : 0.003 0.023 1953 Dihedral : 3.544 20.949 1505 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer Outliers : 5.17 % 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: 3.55 (0.22), residues: 1358 helix: 2.92 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : -0.28 (0.35), residues: 266 *********************** 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 200 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 133 time to evaluate : 2.200 Fit side-chains outliers start: 67 outliers final: 45 residues processed: 182 average time/residue: 1.2975 time to fit residues: 256.0340 Evaluate side-chains 173 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 128 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 36 residues processed: 9 average time/residue: 0.1874 time to fit residues: 4.6904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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 E 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 11550 Z= 0.294 Angle : 0.492 7.715 15568 Z= 0.264 Chirality : 0.040 0.122 1848 Planarity : 0.003 0.024 1953 Dihedral : 3.734 23.326 1505 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer Outliers : 5.79 % 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: 3.36 (0.22), residues: 1358 helix: 2.78 (0.15), residues: 1085 sheet: None (None), residues: 0 loop : -0.18 (0.34), residues: 273 *********************** 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 231 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 156 time to evaluate : 1.511 Fit side-chains outliers start: 75 outliers final: 49 residues processed: 207 average time/residue: 1.3298 time to fit residues: 296.3164 Evaluate side-chains 201 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 152 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 37 residues processed: 12 average time/residue: 0.3575 time to fit residues: 7.3475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 F 141 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 11550 Z= 0.239 Angle : 0.469 8.344 15568 Z= 0.253 Chirality : 0.039 0.116 1848 Planarity : 0.003 0.023 1953 Dihedral : 3.682 22.218 1505 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer Outliers : 5.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.33 (0.22), residues: 1358 helix: 2.77 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : -0.30 (0.35), residues: 266 *********************** 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 215 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 146 time to evaluate : 1.529 Fit side-chains outliers start: 69 outliers final: 50 residues processed: 196 average time/residue: 1.2217 time to fit residues: 259.9897 Evaluate side-chains 195 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 145 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 39 residues processed: 11 average time/residue: 0.1830 time to fit residues: 5.0991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 112 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 126 optimal weight: 0.0040 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 F 141 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 11550 Z= 0.172 Angle : 0.437 9.240 15568 Z= 0.235 Chirality : 0.037 0.119 1848 Planarity : 0.003 0.025 1953 Dihedral : 3.491 19.152 1505 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 4.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.58 (0.22), residues: 1358 helix: 2.95 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : -0.27 (0.35), residues: 266 *********************** 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 187 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 127 time to evaluate : 1.466 Fit side-chains outliers start: 60 outliers final: 45 residues processed: 173 average time/residue: 1.3110 time to fit residues: 245.3637 Evaluate side-chains 167 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 122 time to evaluate : 1.534 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 37 residues processed: 9 average time/residue: 0.4443 time to fit residues: 6.9559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN C 178 GLN E 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11550 Z= 0.191 Angle : 0.449 9.665 15568 Z= 0.241 Chirality : 0.038 0.127 1848 Planarity : 0.003 0.024 1953 Dihedral : 3.488 19.007 1505 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer Outliers : 3.86 % 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: 3.55 (0.22), residues: 1358 helix: 2.92 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : -0.24 (0.35), residues: 266 ********************** 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 176 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 126 time to evaluate : 1.557 Fit side-chains outliers start: 50 outliers final: 44 residues processed: 167 average time/residue: 1.2838 time to fit residues: 231.8353 Evaluate side-chains 166 residues out of total 1309 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 122 time to evaluate : 1.542 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 36 residues processed: 8 average time/residue: 0.1805 time to fit residues: 4.3549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 108 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 178 GLN E 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.128127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.108879 restraints weight = 12189.031| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.64 r_work: 0.3080 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3335 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= 0.171 Angle : 0.440 10.805 15568 Z= 0.235 Chirality : 0.037 0.124 1848 Planarity : 0.003 0.025 1953 Dihedral : 3.416 17.792 1505 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 3.94 % 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: 3.64 (0.22), residues: 1358 helix: 2.98 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : -0.23 (0.35), residues: 266 =============================================================================== Job complete usr+sys time: 4404.60 seconds wall clock time: 78 minutes 50.62 seconds (4730.62 seconds total)