Starting phenix.real_space_refine (version: 1.21rc1) on Tue Aug 15 21:00:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzx_33533/08_2023/7xzx_33533.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzx_33533/08_2023/7xzx_33533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzx_33533/08_2023/7xzx_33533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzx_33533/08_2023/7xzx_33533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzx_33533/08_2023/7xzx_33533.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xzx_33533/08_2023/7xzx_33533.pdb" } resolution = 4.53 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= 0.003 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 P 341 5.49 5 S 78 5.16 5 C 10946 2.51 5 N 3618 2.21 5 O 4287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "K TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 180": "OE1" <-> "OE2" Residue "K ASP 186": "OD1" <-> "OD2" Residue "K GLU 198": "OE1" <-> "OE2" Residue "K GLU 204": "OE1" <-> "OE2" Residue "K TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 207": "OD1" <-> "OD2" Residue "K ARG 209": "NH1" <-> "NH2" Residue "K GLU 224": "OE1" <-> "OE2" Residue "K GLU 258": "OE1" <-> "OE2" Residue "L TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 186": "OD1" <-> "OD2" Residue "L GLU 198": "OE1" <-> "OE2" Residue "L GLU 204": "OE1" <-> "OE2" Residue "L TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 207": "OD1" <-> "OD2" Residue "L ARG 209": "NH1" <-> "NH2" Residue "L GLU 221": "OE1" <-> "OE2" Residue "M TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 180": "OE1" <-> "OE2" Residue "M ASP 186": "OD1" <-> "OD2" Residue "M GLU 198": "OE1" <-> "OE2" Residue "M GLU 204": "OE1" <-> "OE2" Residue "M TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 207": "OD1" <-> "OD2" Residue "M ARG 209": "NH1" <-> "NH2" Residue "N TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 180": "OE1" <-> "OE2" Residue "N ASP 186": "OD1" <-> "OD2" Residue "N GLU 198": "OE1" <-> "OE2" Residue "N GLU 204": "OE1" <-> "OE2" Residue "N TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 207": "OD1" <-> "OD2" Residue "N ARG 209": "NH1" <-> "NH2" Residue "N GLU 224": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 19270 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3487 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 3507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3507 Classifications: {'DNA': 171} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 170} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1555 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "L" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1555 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "M" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1555 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "N" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1555 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 14, 'TRANS': 183} Time building chain proxies: 10.01, per 1000 atoms: 0.52 Number of scatterers: 19270 At special positions: 0 Unit cell: (170.5, 157.3, 125.4, 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 78 16.00 P 341 15.00 O 4287 8.00 N 3618 7.00 C 10946 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: 9.83 Conformation dependent library (CDL) restraints added in 2.0 seconds 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 18 sheets defined 42.9% alpha, 15.2% beta 166 base pairs and 300 stacking pairs defined. Time for finding SS restraints: 9.07 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.096A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.292A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.117A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.994A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.537A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.553A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.880A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.267A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.523A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 122 Processing helix chain 'K' and resid 165 through 169 Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'K' and resid 277 through 288 Processing helix chain 'K' and resid 289 through 291 No H-bonds generated for 'chain 'K' and resid 289 through 291' Processing helix chain 'L' and resid 165 through 169 Processing helix chain 'L' and resid 176 through 182 Processing helix chain 'L' and resid 277 through 288 Processing helix chain 'L' and resid 289 through 291 No H-bonds generated for 'chain 'L' and resid 289 through 291' Processing helix chain 'M' and resid 165 through 169 Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'M' and resid 277 through 289 Processing helix chain 'N' and resid 165 through 169 Processing helix chain 'N' and resid 176 through 182 Processing helix chain 'N' and resid 277 through 288 Processing helix chain 'N' and resid 289 through 291 No H-bonds generated for 'chain 'N' and resid 289 through 291' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.999A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.083A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.757A pdb=" N ILE C 78 " --> pdb=" O GLY D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.501A pdb=" N TYR F 98 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.760A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.342A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.547A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 110 through 112 Processing sheet with id=AB3, first strand: chain 'K' and resid 124 through 127 removed outlier: 6.213A pdb=" N LEU K 257 " --> pdb=" O LEU K 265 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG K 267 " --> pdb=" O ILE K 255 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE K 255 " --> pdb=" O ARG K 267 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER K 269 " --> pdb=" O THR K 253 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR K 253 " --> pdb=" O SER K 269 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU K 271 " --> pdb=" O ILE K 251 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE K 251 " --> pdb=" O GLU K 271 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ALA K 161 " --> pdb=" O HIS K 214 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N HIS K 214 " --> pdb=" O ALA K 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 110 through 112 Processing sheet with id=AB5, first strand: chain 'L' and resid 124 through 127 removed outlier: 3.802A pdb=" N ILE L 251 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA L 161 " --> pdb=" O HIS L 214 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N HIS L 214 " --> pdb=" O ALA L 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 110 through 112 Processing sheet with id=AB7, first strand: chain 'M' and resid 124 through 127 removed outlier: 3.832A pdb=" N ILE M 251 " --> pdb=" O VAL M 272 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA M 161 " --> pdb=" O HIS M 214 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS M 214 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 110 through 112 Processing sheet with id=AB9, first strand: chain 'N' and resid 124 through 127 removed outlier: 3.840A pdb=" N ILE N 251 " --> pdb=" O VAL N 272 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ALA N 161 " --> pdb=" O HIS N 214 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N HIS N 214 " --> pdb=" O ALA N 161 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 429 hydrogen bonds 854 hydrogen bond angles 0 basepair planarities 166 basepair parallelities 300 stacking parallelities Total time for adding SS restraints: 7.64 Time building geometry restraints manager: 10.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3653 1.33 - 1.46: 6944 1.46 - 1.59: 8955 1.59 - 1.71: 679 1.71 - 1.84: 112 Bond restraints: 20343 Sorted by residual: bond pdb=" C PRO L 222 " pdb=" O PRO L 222 " ideal model delta sigma weight residual 1.246 1.213 0.033 8.50e-03 1.38e+04 1.48e+01 bond pdb=" C PRO M 222 " pdb=" O PRO M 222 " ideal model delta sigma weight residual 1.240 1.202 0.039 1.12e-02 7.97e+03 1.20e+01 bond pdb=" CA PRO K 190 " pdb=" C PRO K 190 " ideal model delta sigma weight residual 1.514 1.533 -0.019 5.50e-03 3.31e+04 1.15e+01 bond pdb=" N VAL K 122 " pdb=" CA VAL K 122 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N VAL N 225 " pdb=" CA VAL N 225 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.24e-02 6.50e+03 1.06e+01 ... (remaining 20338 not shown) Histogram of bond angle deviations from ideal: 96.58 - 104.03: 1235 104.03 - 111.48: 9935 111.48 - 118.93: 6933 118.93 - 126.38: 9808 126.38 - 133.83: 1047 Bond angle restraints: 28958 Sorted by residual: angle pdb=" O PRO L 190 " pdb=" C PRO L 190 " pdb=" N PRO L 191 " ideal model delta sigma weight residual 121.31 123.34 -2.03 4.60e-01 4.73e+00 1.96e+01 angle pdb=" N LEU M 265 " pdb=" CA LEU M 265 " pdb=" C LEU M 265 " ideal model delta sigma weight residual 113.88 108.69 5.19 1.23e+00 6.61e-01 1.78e+01 angle pdb=" O PRO K 190 " pdb=" C PRO K 190 " pdb=" N PRO K 191 " ideal model delta sigma weight residual 121.31 123.16 -1.85 4.60e-01 4.73e+00 1.62e+01 angle pdb=" N GLN E 76 " pdb=" CA GLN E 76 " pdb=" CB GLN E 76 " ideal model delta sigma weight residual 110.32 117.14 -6.82 1.70e+00 3.46e-01 1.61e+01 angle pdb=" O PRO M 190 " pdb=" C PRO M 190 " pdb=" N PRO M 191 " ideal model delta sigma weight residual 121.31 123.14 -1.83 4.60e-01 4.73e+00 1.58e+01 ... (remaining 28953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.70: 9109 30.70 - 61.41: 1962 61.41 - 92.11: 63 92.11 - 122.81: 1 122.81 - 153.51: 1 Dihedral angle restraints: 11136 sinusoidal: 6632 harmonic: 4504 Sorted by residual: dihedral pdb=" C4' DC J 33 " pdb=" C3' DC J 33 " pdb=" O3' DC J 33 " pdb=" P DC J 34 " ideal model delta sinusoidal sigma weight residual 220.00 66.49 153.51 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA TYR M 236 " pdb=" C TYR M 236 " pdb=" N MET M 237 " pdb=" CA MET M 237 " ideal model delta harmonic sigma weight residual -180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA TYR K 236 " pdb=" C TYR K 236 " pdb=" N MET K 237 " pdb=" CA MET K 237 " ideal model delta harmonic sigma weight residual 180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 11133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2194 0.051 - 0.102: 774 0.102 - 0.153: 193 0.153 - 0.204: 77 0.204 - 0.256: 9 Chirality restraints: 3247 Sorted by residual: chirality pdb=" CA ARG L 248 " pdb=" N ARG L 248 " pdb=" C ARG L 248 " pdb=" CB ARG L 248 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ARG N 248 " pdb=" N ARG N 248 " pdb=" C ARG N 248 " pdb=" CB ARG N 248 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA GLU C 61 " pdb=" N GLU C 61 " pdb=" C GLU C 61 " pdb=" CB GLU C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 3244 not shown) Planarity restraints: 2533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 52 " 0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C ALA G 52 " -0.077 2.00e-02 2.50e+03 pdb=" O ALA G 52 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA G 53 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C LYS F 59 " -0.053 2.00e-02 2.50e+03 pdb=" O LYS F 59 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL F 60 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 32 " 0.038 2.00e-02 2.50e+03 1.74e-02 7.61e+00 pdb=" N1 DT I 32 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DT I 32 " -0.010 2.00e-02 2.50e+03 pdb=" O2 DT I 32 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DT I 32 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DT I 32 " 0.006 2.00e-02 2.50e+03 pdb=" O4 DT I 32 " 0.024 2.00e-02 2.50e+03 pdb=" C5 DT I 32 " -0.010 2.00e-02 2.50e+03 pdb=" C7 DT I 32 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DT I 32 " -0.021 2.00e-02 2.50e+03 ... (remaining 2530 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 39 2.33 - 2.97: 8793 2.97 - 3.61: 30401 3.61 - 4.26: 51634 4.26 - 4.90: 76401 Nonbonded interactions: 167268 Sorted by model distance: nonbonded pdb=" NZ LYS C 75 " pdb=" P DA J 157 " model vdw 1.688 3.480 nonbonded pdb=" CD1 LEU G 23 " pdb=" OE1 GLU G 56 " model vdw 1.717 3.460 nonbonded pdb=" NZ LYS C 75 " pdb=" OP1 DA J 157 " model vdw 1.752 2.520 nonbonded pdb=" NH2 ARG G 17 " pdb=" OP2 DA J 55 " model vdw 1.851 2.520 nonbonded pdb=" NH2 ARG F 36 " pdb=" OP1 DA J 85 " model vdw 1.906 2.520 ... (remaining 167263 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 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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=0.00 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: 0.510 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: 0.020 Extract box with map and model: 4.180 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 59.510 Find NCS groups from input model: 0.980 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3738 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 : 0.006 0.058 20343 Z= 0.370 Angle : 0.987 8.665 28958 Z= 0.645 Chirality : 0.060 0.256 3247 Planarity : 0.005 0.045 2533 Dihedral : 25.638 153.511 8236 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.19), residues: 1530 helix: 0.79 (0.18), residues: 629 sheet: 0.45 (0.26), residues: 312 loop : 0.31 (0.25), residues: 589 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 266 time to evaluate : 1.732 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 outliers start: 2 outliers final: 0 residues processed: 266 average time/residue: 0.3457 time to fit residues: 134.5186 Evaluate side-chains 138 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.767 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.6980 chunk 137 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 142 optimal weight: 50.0000 chunk 55 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 106 optimal weight: 40.0000 chunk 165 optimal weight: 0.0370 overall best weight: 4.5466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 ASN L 263 ASN L 288 ASN ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 235 ASN ** M 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 288 ASN N 268 ASN N 288 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4067 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.096 20343 Z= 0.288 Angle : 0.649 8.031 28958 Z= 0.378 Chirality : 0.040 0.263 3247 Planarity : 0.005 0.037 2533 Dihedral : 29.643 155.671 5179 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer Outliers : 0.30 % 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: 1.50 (0.20), residues: 1530 helix: 1.69 (0.19), residues: 627 sheet: 0.68 (0.26), residues: 324 loop : 0.57 (0.25), residues: 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 181 time to evaluate : 1.803 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 outliers start: 4 outliers final: 1 residues processed: 184 average time/residue: 0.3111 time to fit residues: 88.2441 Evaluate side-chains 122 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.905 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2159 time to fit residues: 2.6555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 147 optimal weight: 50.0000 chunk 164 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN C 24 GLN D 44 GLN E 68 GLN F 75 HIS H 46 HIS L 268 ASN M 100 GLN ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 178 HIS M 239 ASN M 268 ASN N 193 HIS N 239 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4266 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 20343 Z= 0.250 Angle : 0.624 7.958 28958 Z= 0.360 Chirality : 0.039 0.220 3247 Planarity : 0.005 0.064 2533 Dihedral : 29.723 155.146 5179 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 1530 helix: 1.73 (0.19), residues: 624 sheet: 0.76 (0.27), residues: 324 loop : 0.40 (0.25), residues: 582 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 1.637 Fit side-chains 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: 168 average time/residue: 0.3004 time to fit residues: 77.9088 Evaluate side-chains 118 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2170 time to fit residues: 2.3486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.0040 chunk 124 optimal weight: 40.0000 chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 166 optimal weight: 50.0000 chunk 175 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 overall best weight: 5.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 239 ASN L 168 HIS L 239 ASN M 104 GLN N 100 GLN N 214 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4673 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.092 20343 Z= 0.321 Angle : 0.684 10.862 28958 Z= 0.386 Chirality : 0.041 0.313 3247 Planarity : 0.006 0.110 2533 Dihedral : 29.734 162.213 5179 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.21), residues: 1530 helix: 1.45 (0.20), residues: 625 sheet: 0.66 (0.27), residues: 328 loop : 0.33 (0.25), residues: 577 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 1.743 Fit side-chains 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: 146 average time/residue: 0.3219 time to fit residues: 73.3139 Evaluate side-chains 93 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 1.708 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2217 time to fit residues: 2.5279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 50.0000 chunk 150 optimal weight: 40.0000 chunk 121 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 89 optimal weight: 30.0000 chunk 157 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 100 GLN ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 233 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4659 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 20343 Z= 0.189 Angle : 0.558 8.516 28958 Z= 0.322 Chirality : 0.037 0.169 3247 Planarity : 0.004 0.032 2533 Dihedral : 29.819 159.076 5179 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.21), residues: 1530 helix: 1.90 (0.20), residues: 626 sheet: 0.92 (0.29), residues: 308 loop : 0.23 (0.25), residues: 596 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.901 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 outliers start: 1 outliers final: 1 residues processed: 137 average time/residue: 0.3120 time to fit residues: 66.0903 Evaluate side-chains 94 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 1.817 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1938 time to fit residues: 2.4038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 9.9990 chunk 158 optimal weight: 40.0000 chunk 34 optimal weight: 0.0670 chunk 103 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 235 ASN L 268 ASN N 233 HIS N 235 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4836 moved from start: 0.7374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 20343 Z= 0.261 Angle : 0.597 10.914 28958 Z= 0.345 Chirality : 0.037 0.168 3247 Planarity : 0.004 0.043 2533 Dihedral : 29.682 161.110 5179 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.21), residues: 1530 helix: 1.84 (0.20), residues: 626 sheet: 0.82 (0.28), residues: 328 loop : 0.17 (0.25), residues: 576 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 0.3225 time to fit residues: 59.6812 Evaluate side-chains 81 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.611 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2111 time to fit residues: 2.4510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 128 optimal weight: 40.0000 chunk 99 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 overall best weight: 7.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN F 75 HIS ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 214 HIS L 235 ASN ** M 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5032 moved from start: 0.9046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.106 20343 Z= 0.336 Angle : 0.703 14.252 28958 Z= 0.397 Chirality : 0.042 0.305 3247 Planarity : 0.006 0.146 2533 Dihedral : 30.049 163.177 5179 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: 0.98 (0.21), residues: 1530 helix: 1.39 (0.20), residues: 628 sheet: 0.72 (0.29), residues: 316 loop : -0.09 (0.25), residues: 586 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3174 time to fit residues: 48.9046 Evaluate side-chains 69 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.793 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 20.0000 chunk 70 optimal weight: 0.0040 chunk 104 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 40.0000 chunk 33 optimal weight: 0.9980 chunk 111 optimal weight: 0.0020 chunk 119 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS ** K 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 235 ASN M 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4981 moved from start: 0.9243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 20343 Z= 0.201 Angle : 0.599 11.767 28958 Z= 0.343 Chirality : 0.038 0.404 3247 Planarity : 0.004 0.062 2533 Dihedral : 29.988 165.087 5179 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: 1.17 (0.21), residues: 1530 helix: 1.70 (0.21), residues: 629 sheet: 0.75 (0.29), residues: 316 loop : -0.13 (0.25), residues: 585 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3462 time to fit residues: 53.9948 Evaluate side-chains 68 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 50.0000 chunk 168 optimal weight: 0.8980 chunk 153 optimal weight: 0.0000 chunk 163 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 128 optimal weight: 30.0000 chunk 50 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 154 optimal weight: 30.0000 chunk 162 optimal weight: 10.0000 overall best weight: 6.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS L 179 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5096 moved from start: 1.0080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 20343 Z= 0.296 Angle : 0.650 14.252 28958 Z= 0.370 Chirality : 0.040 0.278 3247 Planarity : 0.006 0.168 2533 Dihedral : 29.850 167.338 5179 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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: 0.95 (0.21), residues: 1530 helix: 1.53 (0.20), residues: 627 sheet: 0.62 (0.29), residues: 316 loop : -0.26 (0.25), residues: 587 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.3311 time to fit residues: 47.7078 Evaluate side-chains 67 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.911 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 105 optimal weight: 40.0000 chunk 82 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 144 optimal weight: 40.0000 chunk 14 optimal weight: 3.9990 chunk 111 optimal weight: 30.0000 chunk 88 optimal weight: 40.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5094 moved from start: 1.0493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 20343 Z= 0.253 Angle : 0.617 13.323 28958 Z= 0.352 Chirality : 0.039 0.341 3247 Planarity : 0.006 0.142 2533 Dihedral : 29.960 171.079 5179 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: 0.95 (0.21), residues: 1530 helix: 1.65 (0.20), residues: 626 sheet: 0.64 (0.30), residues: 288 loop : -0.38 (0.25), residues: 616 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3060 Ramachandran restraints generated. 1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.3261 time to fit residues: 48.2669 Evaluate side-chains 67 residues out of total 1347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.848 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 148 optimal weight: 40.0000 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.063243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.032128 restraints weight = 180020.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.031634 restraints weight = 109729.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.031789 restraints weight = 75690.785| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 1.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 20343 Z= 0.213 Angle : 0.596 12.220 28958 Z= 0.340 Chirality : 0.038 0.276 3247 Planarity : 0.005 0.092 2533 Dihedral : 29.828 171.777 5179 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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: 1.09 (0.22), residues: 1530 helix: 1.78 (0.21), residues: 627 sheet: 0.74 (0.30), residues: 296 loop : -0.35 (0.25), residues: 607 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2829.87 seconds wall clock time: 53 minutes 8.49 seconds (3188.49 seconds total)