Starting phenix.real_space_refine on Mon Dec 11 23:11:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8udg_42149/12_2023/8udg_42149.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8udg_42149/12_2023/8udg_42149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8udg_42149/12_2023/8udg_42149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8udg_42149/12_2023/8udg_42149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8udg_42149/12_2023/8udg_42149.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8udg_42149/12_2023/8udg_42149.pdb" } resolution = 4.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 43 5.16 5 C 6158 2.51 5 N 1683 2.21 5 O 2013 1.98 5 H 9627 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 19524 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2383 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "B" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2384 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "C" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 2385 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "H" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3160 Classifications: {'peptide': 211} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 197} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3025 Classifications: {'peptide': 209} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3161 Classifications: {'peptide': 211} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3026 Classifications: {'peptide': 209} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.07, per 1000 atoms: 0.46 Number of scatterers: 19524 At special positions: 0 Unit cell: (99, 176.344, 165.516, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 O 2013 8.00 N 1683 7.00 C 6158 6.00 H 9627 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 146 " - pdb=" SG CYS M 202 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 138 " - pdb=" SG CYS N 197 " distance=2.04 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: 15.80 Conformation dependent library (CDL) restraints added in 2.0 seconds 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2432 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 25 sheets defined 28.5% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 26 through 105 removed outlier: 3.700A pdb=" N HIS A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 34 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA A 36 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 125 Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.579A pdb=" N GLY A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 105 removed outlier: 3.543A pdb=" N HIS B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 125 Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.699A pdb=" N GLY B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 105 removed outlier: 3.712A pdb=" N HIS C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 125 Processing helix chain 'C' and resid 145 through 155 removed outlier: 3.625A pdb=" N GLY C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 191 through 195 removed outlier: 3.623A pdb=" N LEU H 195 " --> pdb=" O SER H 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 186 through 192 removed outlier: 3.582A pdb=" N SER L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS L 192 " --> pdb=" O GLN L 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'M' and resid 191 through 195 removed outlier: 3.618A pdb=" N LEU M 195 " --> pdb=" O SER M 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 85 Processing helix chain 'N' and resid 125 through 131 Processing helix chain 'N' and resid 186 through 191 removed outlier: 3.665A pdb=" N SER N 191 " --> pdb=" O GLU N 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 134 removed outlier: 6.633A pdb=" N CYS A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AA3, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.628A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.020A pdb=" N CYS H 96 " --> pdb=" O TRP H 109 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TRP H 109 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG H 98 " --> pdb=" O ASP H 107 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 126 through 130 removed outlier: 5.005A pdb=" N ALA H 143 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL H 190 " --> pdb=" O ALA H 143 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 126 through 130 removed outlier: 5.005A pdb=" N ALA H 143 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL H 190 " --> pdb=" O ALA H 143 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 157 through 160 removed outlier: 4.765A pdb=" N TYR H 200 " --> pdb=" O VAL H 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.416A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.416A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB4, first strand: chain 'L' and resid 120 through 122 removed outlier: 5.940A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 157 through 158 Processing sheet with id=AB6, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.649A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.948A pdb=" N CYS M 96 " --> pdb=" O TRP M 109 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TRP M 109 " --> pdb=" O CYS M 96 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG M 98 " --> pdb=" O ASP M 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 126 through 130 removed outlier: 4.920A pdb=" N ALA M 143 " --> pdb=" O VAL M 190 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL M 190 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLY M 145 " --> pdb=" O VAL M 188 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL M 188 " --> pdb=" O GLY M 145 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU M 147 " --> pdb=" O SER M 186 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SER M 186 " --> pdb=" O LEU M 147 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS M 149 " --> pdb=" O LEU M 184 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU M 184 " --> pdb=" O LYS M 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 126 through 130 removed outlier: 4.920A pdb=" N ALA M 143 " --> pdb=" O VAL M 190 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL M 190 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLY M 145 " --> pdb=" O VAL M 188 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL M 188 " --> pdb=" O GLY M 145 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU M 147 " --> pdb=" O SER M 186 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SER M 186 " --> pdb=" O LEU M 147 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS M 149 " --> pdb=" O LEU M 184 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU M 184 " --> pdb=" O LYS M 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 157 through 160 removed outlier: 4.530A pdb=" N TYR M 200 " --> pdb=" O VAL M 217 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.368A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 9 through 12 Processing sheet with id=AC5, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AC6, first strand: chain 'N' and resid 120 through 122 removed outlier: 6.020A pdb=" N TYR N 176 " --> pdb=" O ASP N 142 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 157 through 158 562 hydrogen bonds defined for protein. 1458 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: 7.53 Time building geometry restraints manager: 16.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9620 1.03 - 1.23: 18 1.23 - 1.42: 4161 1.42 - 1.62: 5854 1.62 - 1.82: 57 Bond restraints: 19710 Sorted by residual: bond pdb=" C SER L 157 " pdb=" N PRO L 158 " ideal model delta sigma weight residual 1.333 1.355 -0.021 1.01e-02 9.80e+03 4.53e+00 bond pdb=" C SER N 157 " pdb=" N PRO N 158 " ideal model delta sigma weight residual 1.333 1.354 -0.021 1.01e-02 9.80e+03 4.22e+00 bond pdb=" N ALA M 120 " pdb=" CA ALA M 120 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.20e-02 6.94e+03 3.28e+00 bond pdb=" C SER M 119 " pdb=" N ALA M 120 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.27e-02 6.20e+03 1.20e+00 bond pdb=" CA VAL H 190 " pdb=" C VAL H 190 " ideal model delta sigma weight residual 1.516 1.526 -0.011 1.11e-02 8.12e+03 9.25e-01 ... (remaining 19705 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.47: 344 106.47 - 113.40: 23839 113.40 - 120.32: 5497 120.32 - 127.25: 5790 127.25 - 134.18: 129 Bond angle restraints: 35599 Sorted by residual: angle pdb=" N VAL H 190 " pdb=" CA VAL H 190 " pdb=" C VAL H 190 " ideal model delta sigma weight residual 109.19 106.11 3.08 8.20e-01 1.49e+00 1.42e+01 angle pdb=" CA VAL H 190 " pdb=" C VAL H 190 " pdb=" N PRO H 191 " ideal model delta sigma weight residual 116.57 120.18 -3.61 9.80e-01 1.04e+00 1.35e+01 angle pdb=" C VAL H 190 " pdb=" CA VAL H 190 " pdb=" CB VAL H 190 " ideal model delta sigma weight residual 109.33 112.38 -3.05 9.80e-01 1.04e+00 9.67e+00 angle pdb=" N GLY H 145 " pdb=" CA GLY H 145 " pdb=" C GLY H 145 " ideal model delta sigma weight residual 111.27 116.40 -5.13 1.67e+00 3.59e-01 9.44e+00 angle pdb=" O SER M 119 " pdb=" C SER M 119 " pdb=" N ALA M 120 " ideal model delta sigma weight residual 122.68 119.07 3.61 1.27e+00 6.20e-01 8.10e+00 ... (remaining 35594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 8475 16.98 - 33.96: 495 33.96 - 50.94: 111 50.94 - 67.92: 33 67.92 - 84.91: 20 Dihedral angle restraints: 9134 sinusoidal: 4835 harmonic: 4299 Sorted by residual: dihedral pdb=" CA SER M 119 " pdb=" C SER M 119 " pdb=" N ALA M 120 " pdb=" CA ALA M 120 " ideal model delta harmonic sigma weight residual 180.00 -155.75 -24.25 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 90 " pdb=" CB CYS N 90 " ideal model delta sinusoidal sigma weight residual 93.00 57.52 35.48 1 1.00e+01 1.00e-02 1.78e+01 dihedral pdb=" CA CYS M 99 " pdb=" C CYS M 99 " pdb=" N VAL M 100 " pdb=" CA VAL M 100 " ideal model delta harmonic sigma weight residual -180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 9131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1071 0.034 - 0.068: 362 0.068 - 0.101: 96 0.101 - 0.135: 45 0.135 - 0.169: 11 Chirality restraints: 1585 Sorted by residual: chirality pdb=" CA VAL M 148 " pdb=" N VAL M 148 " pdb=" C VAL M 148 " pdb=" CB VAL M 148 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA VAL H 190 " pdb=" N VAL H 190 " pdb=" C VAL H 190 " pdb=" CB VAL H 190 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA VAL H 148 " pdb=" N VAL H 148 " pdb=" C VAL H 148 " pdb=" CB VAL H 148 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 1582 not shown) Planarity restraints: 3015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER M 119 " 0.024 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C SER M 119 " -0.079 2.00e-02 2.50e+03 pdb=" O SER M 119 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA M 120 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 33 " -0.013 2.00e-02 2.50e+03 8.89e-03 2.37e+00 pdb=" CG TYR M 33 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR M 33 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR M 33 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR M 33 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR M 33 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR M 33 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR M 33 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR M 33 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR M 33 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR M 33 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR M 33 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 79 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C GLU A 79 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU A 79 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 80 " -0.009 2.00e-02 2.50e+03 ... (remaining 3012 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 2170 2.25 - 2.84: 44806 2.84 - 3.42: 50208 3.42 - 4.01: 69800 4.01 - 4.60: 107200 Nonbonded interactions: 274184 Sorted by model distance: nonbonded pdb=" H SER H 162 " pdb=" OD1 ASN H 203 " model vdw 1.662 1.850 nonbonded pdb=" H GLN L 171 " pdb=" O LYS L 175 " model vdw 1.664 1.850 nonbonded pdb=" O ASP B 37 " pdb=" HG1 THR B 41 " model vdw 1.674 1.850 nonbonded pdb=" OE1 GLN A 42 " pdb=" H ILE C 172 " model vdw 1.680 1.850 nonbonded pdb=" H GLY M 15 " pdb=" O LEU M 86 " model vdw 1.685 1.850 ... (remaining 274179 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' and (resid 23 through 135 or (resid 136 and (name N or name CA or nam \ e C or name O or name HA2 or name HA3)) or resid 137 through 181)) selection = (chain 'C' and (resid 23 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name H \ B2 or name HB3 or name HD21 or name HD22)) or (resid 136 and (name N or name CA \ or name C or name O or name HA2 or name HA3)) or resid 137 through 181)) } ncs_group { reference = chain 'H' selection = (chain 'M' and (resid 1 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1 or name HE2)) or resid 34 through 219)) } ncs_group { reference = chain 'L' selection = (chain 'N' and (resid 1 through 96 or (resid 97 and (name N or name CA or name C \ or name O or name CB or name OG or name H or name HA or name HB2 or name HB3)) \ or resid 98 through 213)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.310 Extract box with map and model: 4.580 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 64.200 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.004 0.028 10083 Z= 0.226 Angle : 0.649 5.339 13699 Z= 0.377 Chirality : 0.041 0.169 1585 Planarity : 0.005 0.046 1772 Dihedral : 11.434 84.819 3614 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.78 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1293 helix: 0.94 (0.25), residues: 340 sheet: -0.41 (0.23), residues: 456 loop : -0.40 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 50 HIS 0.005 0.001 HIS A 74 PHE 0.009 0.002 PHE A 157 TYR 0.025 0.002 TYR H 33 ARG 0.004 0.001 ARG N 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.5726 time to fit residues: 201.8683 Evaluate side-chains 174 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.446 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10083 Z= 0.190 Angle : 0.529 17.986 13699 Z= 0.289 Chirality : 0.039 0.149 1585 Planarity : 0.004 0.054 1772 Dihedral : 4.236 16.810 1375 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.47 % Favored : 97.37 % Rotamer: Outliers : 0.27 % Allowed : 0.90 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.24), residues: 1293 helix: 2.82 (0.25), residues: 352 sheet: -0.25 (0.23), residues: 458 loop : -0.35 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.007 0.001 HIS B 30 PHE 0.013 0.001 PHE H 101 TYR 0.009 0.001 TYR M 33 ARG 0.003 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 193 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 196 average time/residue: 0.6150 time to fit residues: 158.3577 Evaluate side-chains 160 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 1.599 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.2039 time to fit residues: 3.1037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN L 192 HIS ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 10083 Z= 0.349 Angle : 0.656 9.958 13699 Z= 0.371 Chirality : 0.039 0.134 1585 Planarity : 0.004 0.042 1772 Dihedral : 4.724 21.740 1375 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.41 % Favored : 94.43 % Rotamer: Outliers : 0.18 % Allowed : 2.25 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1293 helix: 1.13 (0.25), residues: 358 sheet: -0.37 (0.24), residues: 446 loop : -0.83 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 152 HIS 0.007 0.002 HIS H 170 PHE 0.016 0.002 PHE H 152 TYR 0.014 0.002 TYR H 95 ARG 0.009 0.001 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 158 average time/residue: 0.6256 time to fit residues: 129.7873 Evaluate side-chains 131 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.586 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2133 time to fit residues: 2.4274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 10083 Z= 0.193 Angle : 0.496 4.416 13699 Z= 0.273 Chirality : 0.038 0.142 1585 Planarity : 0.003 0.037 1772 Dihedral : 4.368 25.649 1375 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.87 % Favored : 95.98 % Rotamer: Outliers : 0.09 % Allowed : 0.81 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1293 helix: 2.22 (0.25), residues: 355 sheet: -0.33 (0.24), residues: 458 loop : -0.77 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 152 HIS 0.004 0.001 HIS A 27 PHE 0.011 0.001 PHE A 167 TYR 0.008 0.001 TYR N 38 ARG 0.002 0.000 ARG H 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.5785 time to fit residues: 121.6717 Evaluate side-chains 135 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10083 Z= 0.188 Angle : 0.493 4.285 13699 Z= 0.273 Chirality : 0.038 0.140 1585 Planarity : 0.003 0.038 1772 Dihedral : 4.325 30.697 1375 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.64 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.23), residues: 1293 helix: 2.41 (0.25), residues: 358 sheet: -0.31 (0.24), residues: 458 loop : -0.78 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 36 HIS 0.004 0.001 HIS M 35 PHE 0.010 0.001 PHE A 167 TYR 0.030 0.001 TYR M 33 ARG 0.003 0.000 ARG M 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.5800 time to fit residues: 122.5934 Evaluate side-chains 134 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.699 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.0870 chunk 110 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 0.0970 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10083 Z= 0.146 Angle : 0.474 5.952 13699 Z= 0.261 Chirality : 0.039 0.145 1585 Planarity : 0.003 0.034 1772 Dihedral : 4.147 23.584 1375 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.87 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.24), residues: 1293 helix: 2.87 (0.26), residues: 358 sheet: -0.21 (0.24), residues: 456 loop : -0.68 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 50 HIS 0.004 0.001 HIS A 27 PHE 0.007 0.001 PHE C 157 TYR 0.027 0.001 TYR H 33 ARG 0.002 0.000 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.5881 time to fit residues: 127.8009 Evaluate side-chains 137 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.635 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10083 Z= 0.214 Angle : 0.518 5.862 13699 Z= 0.289 Chirality : 0.038 0.147 1585 Planarity : 0.003 0.033 1772 Dihedral : 4.309 20.902 1375 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.26 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1293 helix: 2.44 (0.25), residues: 358 sheet: -0.18 (0.24), residues: 446 loop : -0.84 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 152 HIS 0.006 0.001 HIS H 170 PHE 0.008 0.001 PHE H 152 TYR 0.021 0.001 TYR H 33 ARG 0.005 0.001 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.5932 time to fit residues: 119.4439 Evaluate side-chains 127 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.629 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 0.0470 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN H 177 GLN ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10083 Z= 0.195 Angle : 0.509 4.825 13699 Z= 0.280 Chirality : 0.038 0.146 1585 Planarity : 0.003 0.038 1772 Dihedral : 4.237 19.488 1375 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.10 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.23), residues: 1293 helix: 2.42 (0.25), residues: 358 sheet: -0.25 (0.24), residues: 452 loop : -0.85 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 152 HIS 0.004 0.001 HIS H 170 PHE 0.009 0.001 PHE A 157 TYR 0.021 0.001 TYR H 33 ARG 0.004 0.001 ARG M 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.5911 time to fit residues: 116.2034 Evaluate side-chains 131 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.684 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10083 Z= 0.196 Angle : 0.507 5.612 13699 Z= 0.281 Chirality : 0.038 0.152 1585 Planarity : 0.003 0.035 1772 Dihedral : 4.280 19.776 1375 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.10 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1293 helix: 2.29 (0.26), residues: 358 sheet: -0.35 (0.24), residues: 462 loop : -0.91 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 152 HIS 0.004 0.001 HIS H 170 PHE 0.017 0.001 PHE A 157 TYR 0.019 0.001 TYR H 33 ARG 0.004 0.001 ARG H 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.6010 time to fit residues: 119.8298 Evaluate side-chains 132 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.624 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 chunk 10 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10083 Z= 0.145 Angle : 0.488 6.792 13699 Z= 0.264 Chirality : 0.039 0.147 1585 Planarity : 0.003 0.035 1772 Dihedral : 4.123 18.226 1375 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.64 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.24), residues: 1293 helix: 2.47 (0.27), residues: 370 sheet: -0.16 (0.24), residues: 446 loop : -0.86 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP M 160 HIS 0.004 0.001 HIS A 27 PHE 0.021 0.001 PHE H 172 TYR 0.020 0.001 TYR H 33 ARG 0.003 0.000 ARG H 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 33 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue ALA 115 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.6100 time to fit residues: 121.0423 Evaluate side-chains 132 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.408 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 30 optimal weight: 0.2980 chunk 92 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.048852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.034032 restraints weight = 222073.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.036400 restraints weight = 128141.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.038218 restraints weight = 84162.515| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10083 Z= 0.138 Angle : 0.471 5.031 13699 Z= 0.255 Chirality : 0.039 0.144 1585 Planarity : 0.003 0.039 1772 Dihedral : 4.005 17.778 1375 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.49 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.24), residues: 1293 helix: 2.65 (0.27), residues: 370 sheet: -0.12 (0.24), residues: 446 loop : -0.73 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.004 0.001 HIS A 27 PHE 0.008 0.001 PHE A 157 TYR 0.020 0.001 TYR H 33 ARG 0.003 0.000 ARG H 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4589.90 seconds wall clock time: 84 minutes 22.99 seconds (5062.99 seconds total)