Starting phenix.real_space_refine (version: dev) on Sat Feb 18 05:57:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ubb_26437/02_2023/7ubb_26437.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ubb_26437/02_2023/7ubb_26437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ubb_26437/02_2023/7ubb_26437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ubb_26437/02_2023/7ubb_26437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ubb_26437/02_2023/7ubb_26437.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ubb_26437/02_2023/7ubb_26437.pdb" } resolution = 4.5 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= 0.026 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 Process input model Symmetric amino acids flipped Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7448 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 931 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 931 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 931 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 931 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 931 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 931 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 931 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 931 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 4.82, per 1000 atoms: 0.65 Number of scatterers: 7448 At special positions: 0 Unit cell: (96.193, 92.597, 151.032, 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 24 16.00 O 1352 8.00 N 1256 7.00 C 4816 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: 3.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 16 sheets defined 40.3% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'C' and resid 110 through 121 removed outlier: 3.662A pdb=" N GLY C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 189 Processing helix chain 'C' and resid 193 through 199 removed outlier: 4.055A pdb=" N LYS C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS C 198 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 216 removed outlier: 3.595A pdb=" N TRP C 216 " --> pdb=" O MET C 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.662A pdb=" N GLY D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 189 Processing helix chain 'D' and resid 193 through 199 removed outlier: 4.054A pdb=" N LYS D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS D 198 " --> pdb=" O PHE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 216 removed outlier: 3.595A pdb=" N TRP D 216 " --> pdb=" O MET D 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.663A pdb=" N GLY E 121 " --> pdb=" O ALA E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 189 Processing helix chain 'E' and resid 193 through 199 removed outlier: 4.054A pdb=" N LYS E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS E 198 " --> pdb=" O PHE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 216 removed outlier: 3.596A pdb=" N TRP E 216 " --> pdb=" O MET E 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 121 removed outlier: 3.662A pdb=" N GLY F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 189 Processing helix chain 'F' and resid 193 through 199 removed outlier: 4.055A pdb=" N LYS F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS F 198 " --> pdb=" O PHE F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 216 removed outlier: 3.595A pdb=" N TRP F 216 " --> pdb=" O MET F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 121 removed outlier: 3.661A pdb=" N GLY G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 189 Processing helix chain 'G' and resid 193 through 199 removed outlier: 4.054A pdb=" N LYS G 197 " --> pdb=" O ASP G 193 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS G 198 " --> pdb=" O PHE G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 216 removed outlier: 3.596A pdb=" N TRP G 216 " --> pdb=" O MET G 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 121 removed outlier: 3.661A pdb=" N GLY H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 189 Processing helix chain 'H' and resid 193 through 199 removed outlier: 4.054A pdb=" N LYS H 197 " --> pdb=" O ASP H 193 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS H 198 " --> pdb=" O PHE H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 216 removed outlier: 3.595A pdb=" N TRP H 216 " --> pdb=" O MET H 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 121 removed outlier: 3.661A pdb=" N GLY I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 189 Processing helix chain 'I' and resid 193 through 199 removed outlier: 4.055A pdb=" N LYS I 197 " --> pdb=" O ASP I 193 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS I 198 " --> pdb=" O PHE I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 216 removed outlier: 3.595A pdb=" N TRP I 216 " --> pdb=" O MET I 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 121 removed outlier: 3.662A pdb=" N GLY J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 189 Processing helix chain 'J' and resid 193 through 199 removed outlier: 4.054A pdb=" N LYS J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS J 198 " --> pdb=" O PHE J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 216 removed outlier: 3.595A pdb=" N TRP J 216 " --> pdb=" O MET J 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 123 through 132 Processing sheet with id=AA2, first strand: chain 'C' and resid 136 through 139 removed outlier: 7.167A pdb=" N GLU C 147 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 123 through 132 Processing sheet with id=AA4, first strand: chain 'D' and resid 136 through 139 removed outlier: 7.167A pdb=" N GLU D 147 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 123 through 132 Processing sheet with id=AA6, first strand: chain 'E' and resid 136 through 139 removed outlier: 7.167A pdb=" N GLU E 147 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 123 through 132 Processing sheet with id=AA8, first strand: chain 'F' and resid 136 through 139 removed outlier: 7.167A pdb=" N GLU F 147 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 123 through 132 Processing sheet with id=AB1, first strand: chain 'G' and resid 136 through 139 removed outlier: 7.168A pdb=" N GLU G 147 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 123 through 132 Processing sheet with id=AB3, first strand: chain 'H' and resid 136 through 139 removed outlier: 7.167A pdb=" N GLU H 147 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 123 through 132 Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 139 removed outlier: 7.167A pdb=" N GLU I 147 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 123 through 132 Processing sheet with id=AB7, first strand: chain 'J' and resid 136 through 139 removed outlier: 7.167A pdb=" N GLU J 147 " --> pdb=" O LEU J 137 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 963 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2304 1.35 - 1.46: 1883 1.46 - 1.58: 3373 1.58 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 7600 Sorted by residual: bond pdb=" CA ASP G 151 " pdb=" CB ASP G 151 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 8.08e-01 bond pdb=" CA ASP D 151 " pdb=" CB ASP D 151 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.81e-01 bond pdb=" CA ASP J 151 " pdb=" CB ASP J 151 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.80e-01 bond pdb=" CA ASP H 151 " pdb=" CB ASP H 151 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.76e-01 bond pdb=" CA ASP C 151 " pdb=" CB ASP C 151 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.60e-01 ... (remaining 7595 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.93: 72 106.93 - 113.69: 4048 113.69 - 120.44: 3115 120.44 - 127.20: 2885 127.20 - 133.96: 80 Bond angle restraints: 10200 Sorted by residual: angle pdb=" C LEU H 150 " pdb=" N ASP H 151 " pdb=" CA ASP H 151 " ideal model delta sigma weight residual 121.54 127.71 -6.17 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C LEU F 150 " pdb=" N ASP F 151 " pdb=" CA ASP F 151 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C LEU I 150 " pdb=" N ASP I 151 " pdb=" CA ASP I 151 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C LEU D 150 " pdb=" N ASP D 151 " pdb=" CA ASP D 151 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C LEU G 150 " pdb=" N ASP G 151 " pdb=" CA ASP G 151 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 ... (remaining 10195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.08: 3696 12.08 - 24.17: 528 24.17 - 36.25: 200 36.25 - 48.33: 40 48.33 - 60.42: 40 Dihedral angle restraints: 4504 sinusoidal: 1896 harmonic: 2608 Sorted by residual: dihedral pdb=" CA SER H 214 " pdb=" C SER H 214 " pdb=" N LYS H 215 " pdb=" CA LYS H 215 " ideal model delta harmonic sigma weight residual -180.00 -163.06 -16.94 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA SER C 214 " pdb=" C SER C 214 " pdb=" N LYS C 215 " pdb=" CA LYS C 215 " ideal model delta harmonic sigma weight residual 180.00 -163.08 -16.92 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA SER J 214 " pdb=" C SER J 214 " pdb=" N LYS J 215 " pdb=" CA LYS J 215 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 4501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 589 0.030 - 0.060: 301 0.060 - 0.091: 144 0.091 - 0.121: 38 0.121 - 0.151: 8 Chirality restraints: 1080 Sorted by residual: chirality pdb=" CA ASP I 151 " pdb=" N ASP I 151 " pdb=" C ASP I 151 " pdb=" CB ASP I 151 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ASP D 151 " pdb=" N ASP D 151 " pdb=" C ASP D 151 " pdb=" CB ASP D 151 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ASP H 151 " pdb=" N ASP H 151 " pdb=" C ASP H 151 " pdb=" CB ASP H 151 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 1077 not shown) Planarity restraints: 1248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 216 " -0.010 2.00e-02 2.50e+03 1.00e-02 2.52e+00 pdb=" CG TRP F 216 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP F 216 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 216 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 216 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 216 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 216 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 216 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 216 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 216 " 0.010 2.00e-02 2.50e+03 9.93e-03 2.46e+00 pdb=" CG TRP I 216 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP I 216 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP I 216 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP I 216 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP I 216 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 216 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 216 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 216 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP I 216 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 216 " 0.010 2.00e-02 2.50e+03 9.91e-03 2.46e+00 pdb=" CG TRP G 216 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP G 216 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP G 216 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 216 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 216 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 216 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 216 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 216 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP G 216 " -0.001 2.00e-02 2.50e+03 ... (remaining 1245 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1212 2.77 - 3.30: 7163 3.30 - 3.83: 11913 3.83 - 4.37: 12490 4.37 - 4.90: 21741 Nonbonded interactions: 54519 Sorted by model distance: nonbonded pdb=" ND2 ASN C 127 " pdb=" OE2 GLU D 144 " model vdw 2.231 2.520 nonbonded pdb=" ND2 ASN H 127 " pdb=" OE2 GLU I 144 " model vdw 2.275 2.520 nonbonded pdb=" O LYS F 186 " pdb=" OG SER F 190 " model vdw 2.299 2.440 nonbonded pdb=" O LYS E 186 " pdb=" OG SER E 190 " model vdw 2.299 2.440 nonbonded pdb=" O LYS J 186 " pdb=" OG SER J 190 " model vdw 2.299 2.440 ... (remaining 54514 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set refine NCS operators NCS operators will be refined. Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 4816 2.51 5 N 1256 2.21 5 O 1352 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.060 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: 5.180 Check model and map are aligned: 0.120 Process input model: 23.670 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.070 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 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 : 0.002 0.022 7600 Z= 0.149 Angle : 0.684 6.967 10200 Z= 0.355 Chirality : 0.043 0.151 1080 Planarity : 0.002 0.010 1248 Dihedral : 14.316 60.416 2840 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.26), residues: 880 helix: 1.14 (0.29), residues: 280 sheet: 0.11 (0.33), residues: 272 loop : -3.15 (0.23), residues: 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.255 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2598 time to fit residues: 5.4003 Evaluate side-chains 9 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 0.0770 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 26 optimal weight: 0.0270 chunk 41 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.6076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 7600 Z= 0.119 Angle : 0.536 5.772 10200 Z= 0.286 Chirality : 0.043 0.147 1080 Planarity : 0.002 0.010 1248 Dihedral : 3.632 12.010 984 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.27), residues: 880 helix: 1.20 (0.29), residues: 296 sheet: 0.24 (0.33), residues: 272 loop : -3.23 (0.24), residues: 312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2241 time to fit residues: 9.9344 Evaluate side-chains 28 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.116 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 54 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 0.0570 chunk 64 optimal weight: 0.8980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 7600 Z= 0.156 Angle : 0.574 5.856 10200 Z= 0.307 Chirality : 0.044 0.154 1080 Planarity : 0.003 0.018 1248 Dihedral : 4.055 14.097 984 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.27), residues: 880 helix: 1.01 (0.30), residues: 288 sheet: 0.10 (0.32), residues: 272 loop : -3.35 (0.26), residues: 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2019 time to fit residues: 7.3275 Evaluate side-chains 28 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.119 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.0040 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.0970 chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 0.0770 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.3148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 7600 Z= 0.151 Angle : 0.582 5.793 10200 Z= 0.309 Chirality : 0.044 0.149 1080 Planarity : 0.002 0.014 1248 Dihedral : 4.274 14.459 984 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.28), residues: 880 helix: 0.99 (0.30), residues: 288 sheet: -0.16 (0.30), residues: 272 loop : -3.14 (0.30), residues: 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.132 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1795 time to fit residues: 7.4848 Evaluate side-chains 27 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.122 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.1980 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 0.0060 chunk 35 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 76 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 7600 Z= 0.166 Angle : 0.604 5.569 10200 Z= 0.315 Chirality : 0.043 0.142 1080 Planarity : 0.003 0.016 1248 Dihedral : 4.143 14.822 984 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.28), residues: 880 helix: 1.14 (0.31), residues: 288 sheet: -0.31 (0.29), residues: 272 loop : -3.15 (0.31), residues: 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1603 time to fit residues: 6.2741 Evaluate side-chains 29 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.115 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 70 optimal weight: 0.0020 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 115 GLN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5870 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 7600 Z= 0.139 Angle : 0.538 5.550 10200 Z= 0.282 Chirality : 0.042 0.137 1080 Planarity : 0.002 0.015 1248 Dihedral : 3.689 9.250 984 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.27), residues: 880 helix: 1.15 (0.31), residues: 288 sheet: -0.06 (0.34), residues: 192 loop : -3.07 (0.25), residues: 400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1453 time to fit residues: 5.4229 Evaluate side-chains 27 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.121 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 7600 Z= 0.141 Angle : 0.551 5.580 10200 Z= 0.285 Chirality : 0.042 0.151 1080 Planarity : 0.002 0.016 1248 Dihedral : 3.669 9.910 984 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.26), residues: 880 helix: 1.10 (0.30), residues: 288 sheet: 0.00 (0.34), residues: 192 loop : -3.09 (0.25), residues: 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1320 time to fit residues: 4.8081 Evaluate side-chains 28 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.118 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 0.0270 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 81 optimal weight: 0.0970 chunk 74 optimal weight: 3.9990 overall best weight: 0.9638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 7600 Z= 0.136 Angle : 0.522 4.758 10200 Z= 0.279 Chirality : 0.041 0.115 1080 Planarity : 0.005 0.050 1248 Dihedral : 3.797 11.666 984 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.26), residues: 880 helix: 1.26 (0.30), residues: 280 sheet: 0.02 (0.35), residues: 192 loop : -3.02 (0.25), residues: 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1429 time to fit residues: 5.6223 Evaluate side-chains 27 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.116 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.0030 chunk 81 optimal weight: 0.0010 chunk 47 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 0.0040 chunk 51 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.3208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 140 ASN F 153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.015 7600 Z= 0.132 Angle : 0.589 6.249 10200 Z= 0.302 Chirality : 0.044 0.157 1080 Planarity : 0.004 0.040 1248 Dihedral : 4.106 13.827 984 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.27), residues: 880 helix: 1.29 (0.31), residues: 280 sheet: 0.22 (0.37), residues: 192 loop : -3.02 (0.24), residues: 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.1401 time to fit residues: 5.5737 Evaluate side-chains 28 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.131 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 0.0170 chunk 58 optimal weight: 0.0570 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.015 7600 Z= 0.122 Angle : 0.539 5.544 10200 Z= 0.280 Chirality : 0.042 0.141 1080 Planarity : 0.003 0.032 1248 Dihedral : 3.872 13.812 984 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.27), residues: 880 helix: 1.23 (0.31), residues: 280 sheet: 0.24 (0.38), residues: 192 loop : -3.01 (0.24), residues: 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.1222 time to fit residues: 4.5860 Evaluate side-chains 28 residues out of total 100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.103 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 71 optimal weight: 0.0770 chunk 8 optimal weight: 0.0170 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.192701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.147541 restraints weight = 1588.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.154728 restraints weight = 1039.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.160914 restraints weight = 714.151| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5451 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.015 7600 Z= 0.131 Angle : 0.580 5.435 10200 Z= 0.298 Chirality : 0.043 0.144 1080 Planarity : 0.003 0.022 1248 Dihedral : 4.045 14.166 984 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.27), residues: 880 helix: 1.35 (0.32), residues: 272 sheet: 0.20 (0.39), residues: 192 loop : -2.89 (0.24), residues: 416 =============================================================================== Job complete usr+sys time: 1553.01 seconds wall clock time: 29 minutes 12.97 seconds (1752.97 seconds total)