Starting phenix.real_space_refine (version: dev) on Tue May 17 04:19:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfk_21185/05_2022/6vfk_21185.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfk_21185/05_2022/6vfk_21185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfk_21185/05_2022/6vfk_21185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfk_21185/05_2022/6vfk_21185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfk_21185/05_2022/6vfk_21185.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfk_21185/05_2022/6vfk_21185.pdb" } resolution = 4.25 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= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 37032 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "C" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "D" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "E" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "G" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "I" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "J" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "K" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "L" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "M" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "N" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "O" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "P" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "Q" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "R" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "S" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "T" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "U" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "V" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "W" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "X" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Time building chain proxies: 20.69, per 1000 atoms: 0.56 Number of scatterers: 37032 At special positions: 0 Unit cell: (175.95, 177.1, 173.65, 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 120 16.00 O 7176 8.00 N 6156 7.00 C 23580 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: 17.10 Conformation dependent library (CDL) restraints added in 5.8 seconds 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9336 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 0 sheets defined 91.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'B' and resid 1 through 30 Processing helix chain 'B' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 93 Processing helix chain 'B' and resid 97 through 121 Processing helix chain 'B' and resid 125 through 153 Processing helix chain 'B' and resid 158 through 183 Processing helix chain 'B' and resid 187 through 215 Processing helix chain 'B' and resid 218 through 245 Processing helix chain 'B' and resid 249 through 277 Processing helix chain 'A' and resid 2 through 17 Processing helix chain 'A' and resid 19 through 34 Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 105 through 120 Processing helix chain 'C' and resid 1 through 30 Processing helix chain 'C' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 93 Processing helix chain 'C' and resid 97 through 121 Processing helix chain 'C' and resid 125 through 153 Processing helix chain 'C' and resid 158 through 183 Processing helix chain 'C' and resid 187 through 215 Processing helix chain 'C' and resid 218 through 245 Processing helix chain 'C' and resid 249 through 277 Processing helix chain 'D' and resid 2 through 17 Processing helix chain 'D' and resid 19 through 34 Processing helix chain 'D' and resid 37 through 50 Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'E' and resid 1 through 30 Processing helix chain 'E' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL E 36 " --> pdb=" O THR E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 93 Processing helix chain 'E' and resid 97 through 121 Processing helix chain 'E' and resid 125 through 153 Processing helix chain 'E' and resid 158 through 183 Processing helix chain 'E' and resid 187 through 215 Processing helix chain 'E' and resid 218 through 245 Processing helix chain 'E' and resid 249 through 277 Processing helix chain 'F' and resid 2 through 17 Processing helix chain 'F' and resid 19 through 34 Processing helix chain 'F' and resid 37 through 50 Processing helix chain 'F' and resid 53 through 68 Processing helix chain 'F' and resid 71 through 85 Processing helix chain 'F' and resid 87 through 102 Processing helix chain 'F' and resid 105 through 120 Processing helix chain 'G' and resid 1 through 30 Processing helix chain 'G' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL G 36 " --> pdb=" O THR G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 93 Processing helix chain 'G' and resid 97 through 121 Processing helix chain 'G' and resid 125 through 153 Processing helix chain 'G' and resid 158 through 183 Processing helix chain 'G' and resid 187 through 215 Processing helix chain 'G' and resid 218 through 245 Processing helix chain 'G' and resid 249 through 277 Processing helix chain 'H' and resid 2 through 17 Processing helix chain 'H' and resid 19 through 34 Processing helix chain 'H' and resid 37 through 50 Processing helix chain 'H' and resid 53 through 68 Processing helix chain 'H' and resid 71 through 85 Processing helix chain 'H' and resid 87 through 102 Processing helix chain 'H' and resid 105 through 120 Processing helix chain 'I' and resid 1 through 30 Processing helix chain 'I' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL I 36 " --> pdb=" O THR I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 93 Processing helix chain 'I' and resid 97 through 121 Processing helix chain 'I' and resid 125 through 153 Processing helix chain 'I' and resid 158 through 183 Processing helix chain 'I' and resid 187 through 215 Processing helix chain 'I' and resid 218 through 245 Processing helix chain 'I' and resid 249 through 277 Processing helix chain 'J' and resid 2 through 17 Processing helix chain 'J' and resid 19 through 34 Processing helix chain 'J' and resid 37 through 50 Processing helix chain 'J' and resid 53 through 68 Processing helix chain 'J' and resid 71 through 85 Processing helix chain 'J' and resid 87 through 102 Processing helix chain 'J' and resid 105 through 120 Processing helix chain 'K' and resid 1 through 30 Processing helix chain 'K' and resid 32 through 59 removed outlier: 3.502A pdb=" N VAL K 36 " --> pdb=" O THR K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 93 Processing helix chain 'K' and resid 97 through 121 Processing helix chain 'K' and resid 125 through 153 Processing helix chain 'K' and resid 158 through 183 Processing helix chain 'K' and resid 187 through 215 Processing helix chain 'K' and resid 218 through 245 Processing helix chain 'K' and resid 249 through 277 Processing helix chain 'L' and resid 2 through 17 Processing helix chain 'L' and resid 19 through 34 Processing helix chain 'L' and resid 37 through 50 Processing helix chain 'L' and resid 53 through 68 Processing helix chain 'L' and resid 71 through 85 Processing helix chain 'L' and resid 87 through 102 Processing helix chain 'L' and resid 105 through 120 Processing helix chain 'M' and resid 1 through 30 Processing helix chain 'M' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL M 36 " --> pdb=" O THR M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 93 Processing helix chain 'M' and resid 97 through 121 Processing helix chain 'M' and resid 125 through 153 Processing helix chain 'M' and resid 158 through 183 Processing helix chain 'M' and resid 187 through 215 Processing helix chain 'M' and resid 218 through 245 Processing helix chain 'M' and resid 249 through 277 Processing helix chain 'N' and resid 2 through 17 Processing helix chain 'N' and resid 19 through 34 Processing helix chain 'N' and resid 37 through 50 Processing helix chain 'N' and resid 53 through 68 Processing helix chain 'N' and resid 71 through 85 Processing helix chain 'N' and resid 87 through 102 Processing helix chain 'N' and resid 105 through 120 Processing helix chain 'O' and resid 1 through 30 Processing helix chain 'O' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL O 36 " --> pdb=" O THR O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 93 Processing helix chain 'O' and resid 97 through 121 Processing helix chain 'O' and resid 125 through 153 Processing helix chain 'O' and resid 158 through 183 Processing helix chain 'O' and resid 187 through 215 Processing helix chain 'O' and resid 218 through 245 Processing helix chain 'O' and resid 249 through 277 Processing helix chain 'P' and resid 2 through 17 Processing helix chain 'P' and resid 19 through 34 Processing helix chain 'P' and resid 37 through 50 Processing helix chain 'P' and resid 53 through 68 Processing helix chain 'P' and resid 71 through 85 Processing helix chain 'P' and resid 87 through 102 Processing helix chain 'P' and resid 105 through 120 Processing helix chain 'Q' and resid 1 through 30 Processing helix chain 'Q' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL Q 36 " --> pdb=" O THR Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 93 Processing helix chain 'Q' and resid 97 through 121 Processing helix chain 'Q' and resid 125 through 153 Processing helix chain 'Q' and resid 158 through 183 Processing helix chain 'Q' and resid 187 through 215 Processing helix chain 'Q' and resid 218 through 245 Processing helix chain 'Q' and resid 249 through 277 Processing helix chain 'R' and resid 2 through 17 Processing helix chain 'R' and resid 19 through 34 Processing helix chain 'R' and resid 37 through 50 Processing helix chain 'R' and resid 53 through 68 Processing helix chain 'R' and resid 71 through 85 Processing helix chain 'R' and resid 87 through 102 Processing helix chain 'R' and resid 105 through 120 Processing helix chain 'S' and resid 1 through 30 Processing helix chain 'S' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL S 36 " --> pdb=" O THR S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 93 Processing helix chain 'S' and resid 97 through 121 Processing helix chain 'S' and resid 125 through 153 Processing helix chain 'S' and resid 158 through 183 Processing helix chain 'S' and resid 187 through 215 Processing helix chain 'S' and resid 218 through 245 Processing helix chain 'S' and resid 249 through 277 Processing helix chain 'T' and resid 2 through 17 Processing helix chain 'T' and resid 19 through 34 Processing helix chain 'T' and resid 37 through 50 Processing helix chain 'T' and resid 53 through 68 Processing helix chain 'T' and resid 71 through 85 Processing helix chain 'T' and resid 87 through 102 Processing helix chain 'T' and resid 105 through 120 Processing helix chain 'U' and resid 1 through 30 Processing helix chain 'U' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL U 36 " --> pdb=" O THR U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 93 Processing helix chain 'U' and resid 97 through 121 Processing helix chain 'U' and resid 125 through 153 Processing helix chain 'U' and resid 158 through 183 Processing helix chain 'U' and resid 187 through 215 Processing helix chain 'U' and resid 218 through 245 Processing helix chain 'U' and resid 249 through 277 Processing helix chain 'V' and resid 2 through 17 Processing helix chain 'V' and resid 19 through 34 Processing helix chain 'V' and resid 37 through 50 Processing helix chain 'V' and resid 53 through 68 Processing helix chain 'V' and resid 71 through 85 Processing helix chain 'V' and resid 87 through 102 Processing helix chain 'V' and resid 105 through 120 Processing helix chain 'W' and resid 1 through 30 Processing helix chain 'W' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL W 36 " --> pdb=" O THR W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 93 Processing helix chain 'W' and resid 97 through 121 Processing helix chain 'W' and resid 125 through 153 Processing helix chain 'W' and resid 158 through 183 Processing helix chain 'W' and resid 187 through 215 Processing helix chain 'W' and resid 218 through 245 Processing helix chain 'W' and resid 249 through 277 Processing helix chain 'X' and resid 2 through 17 Processing helix chain 'X' and resid 19 through 34 Processing helix chain 'X' and resid 37 through 50 Processing helix chain 'X' and resid 53 through 68 Processing helix chain 'X' and resid 71 through 85 Processing helix chain 'X' and resid 87 through 102 Processing helix chain 'X' and resid 105 through 120 3588 hydrogen bonds defined for protein. 10764 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: 14.29 Time building geometry restraints manager: 18.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 7435 1.31 - 1.44: 10073 1.44 - 1.57: 19515 1.57 - 1.69: 213 1.69 - 1.82: 240 Bond restraints: 37476 Sorted by residual: bond pdb=" CB HIS M 123 " pdb=" CG HIS M 123 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.27e+01 bond pdb=" CB HIS Q 123 " pdb=" CG HIS Q 123 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.26e+01 bond pdb=" CB HIS E 123 " pdb=" CG HIS E 123 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.25e+01 bond pdb=" CB HIS B 123 " pdb=" CG HIS B 123 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.25e+01 bond pdb=" CB HIS S 123 " pdb=" CG HIS S 123 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.25e+01 ... (remaining 37471 not shown) Histogram of bond angle deviations from ideal: 101.09 - 107.66: 1168 107.66 - 114.23: 20767 114.23 - 120.80: 19318 120.80 - 127.37: 9224 127.37 - 133.94: 151 Bond angle restraints: 50628 Sorted by residual: angle pdb=" C ASP N 34 " pdb=" N PRO N 35 " pdb=" CA PRO N 35 " ideal model delta sigma weight residual 119.82 127.79 -7.97 9.80e-01 1.04e+00 6.61e+01 angle pdb=" C ASP T 34 " pdb=" N PRO T 35 " pdb=" CA PRO T 35 " ideal model delta sigma weight residual 119.82 127.76 -7.94 9.80e-01 1.04e+00 6.56e+01 angle pdb=" C ASP H 34 " pdb=" N PRO H 35 " pdb=" CA PRO H 35 " ideal model delta sigma weight residual 119.82 127.76 -7.94 9.80e-01 1.04e+00 6.56e+01 angle pdb=" C ASP L 34 " pdb=" N PRO L 35 " pdb=" CA PRO L 35 " ideal model delta sigma weight residual 119.82 127.75 -7.93 9.80e-01 1.04e+00 6.55e+01 angle pdb=" C ASP V 34 " pdb=" N PRO V 35 " pdb=" CA PRO V 35 " ideal model delta sigma weight residual 119.82 127.75 -7.93 9.80e-01 1.04e+00 6.55e+01 ... (remaining 50623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 22253 15.11 - 30.22: 739 30.22 - 45.32: 192 45.32 - 60.43: 48 60.43 - 75.54: 48 Dihedral angle restraints: 23280 sinusoidal: 8952 harmonic: 14328 Sorted by residual: dihedral pdb=" CB GLU V 12 " pdb=" CG GLU V 12 " pdb=" CD GLU V 12 " pdb=" OE1 GLU V 12 " ideal model delta sinusoidal sigma weight residual 0.00 -75.54 75.54 1 3.00e+01 1.11e-03 8.00e+00 dihedral pdb=" CB GLU D 12 " pdb=" CG GLU D 12 " pdb=" CD GLU D 12 " pdb=" OE1 GLU D 12 " ideal model delta sinusoidal sigma weight residual 0.00 -75.52 75.52 1 3.00e+01 1.11e-03 8.00e+00 dihedral pdb=" CB GLU P 12 " pdb=" CG GLU P 12 " pdb=" CD GLU P 12 " pdb=" OE1 GLU P 12 " ideal model delta sinusoidal sigma weight residual 0.00 -75.51 75.51 1 3.00e+01 1.11e-03 8.00e+00 ... (remaining 23277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3645 0.072 - 0.145: 1729 0.145 - 0.217: 511 0.217 - 0.289: 57 0.289 - 0.361: 22 Chirality restraints: 5964 Sorted by residual: chirality pdb=" CG LEU P 106 " pdb=" CB LEU P 106 " pdb=" CD1 LEU P 106 " pdb=" CD2 LEU P 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.95 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CG LEU T 106 " pdb=" CB LEU T 106 " pdb=" CD1 LEU T 106 " pdb=" CD2 LEU T 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.95 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CG LEU R 106 " pdb=" CB LEU R 106 " pdb=" CD1 LEU R 106 " pdb=" CD2 LEU R 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.95 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 5961 not shown) Planarity restraints: 6444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR W 148 " 0.082 2.00e-02 2.50e+03 4.52e-02 4.08e+01 pdb=" CG TYR W 148 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR W 148 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR W 148 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR W 148 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR W 148 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR W 148 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR W 148 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 148 " 0.082 2.00e-02 2.50e+03 4.50e-02 4.06e+01 pdb=" CG TYR C 148 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR C 148 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR C 148 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR C 148 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR C 148 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR C 148 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR C 148 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 148 " 0.082 2.00e-02 2.50e+03 4.50e-02 4.06e+01 pdb=" CG TYR Q 148 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 148 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 148 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 148 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 148 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR Q 148 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR Q 148 " 0.072 2.00e-02 2.50e+03 ... (remaining 6441 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 15949 2.89 - 3.39: 42847 3.39 - 3.90: 65743 3.90 - 4.40: 79769 4.40 - 4.90: 121318 Nonbonded interactions: 325626 Sorted by model distance: nonbonded pdb=" OG1 THR W 156 " pdb=" N ASP W 157 " model vdw 2.389 2.520 nonbonded pdb=" OG1 THR U 156 " pdb=" N ASP U 157 " model vdw 2.389 2.520 nonbonded pdb=" OG1 THR I 156 " pdb=" N ASP I 157 " model vdw 2.389 2.520 nonbonded pdb=" OG1 THR O 156 " pdb=" N ASP O 157 " model vdw 2.389 2.520 nonbonded pdb=" OG1 THR E 156 " pdb=" N ASP E 157 " model vdw 2.390 2.520 ... (remaining 325621 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 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 23580 2.51 5 N 6156 2.21 5 O 7176 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: 4.210 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: 0.030 Extract box with map and model: 21.140 Check model and map are aligned: 0.620 Convert atoms to be neutral: 0.350 Process input model: 97.300 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 : 0.021 0.127 37476 Z= 1.336 Angle : 1.410 7.966 50628 Z= 0.968 Chirality : 0.086 0.361 5964 Planarity : 0.009 0.045 6444 Dihedral : 10.301 75.538 13944 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: 2.59 (0.10), residues: 4716 helix: 1.80 (0.06), residues: 4344 sheet: None (None), residues: 0 loop : 1.15 (0.35), residues: 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1316 time to evaluate : 5.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1316 average time/residue: 0.5329 time to fit residues: 1098.2908 Evaluate side-chains 503 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 4.390 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 395 optimal weight: 1.9990 chunk 354 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 239 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 366 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 273 optimal weight: 0.9990 chunk 424 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 HIS ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 ASN K 122 ASN O 122 ASN O 277 ASN Q 122 ASN ** Q 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 ASN U 122 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 37476 Z= 0.227 Angle : 0.569 8.989 50628 Z= 0.308 Chirality : 0.039 0.229 5964 Planarity : 0.004 0.042 6444 Dihedral : 3.775 22.513 5172 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 0.08 % 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: 4.28 (0.11), residues: 4716 helix: 3.00 (0.07), residues: 4380 sheet: None (None), residues: 0 loop : -0.17 (0.35), residues: 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 816 time to evaluate : 4.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 819 average time/residue: 0.4895 time to fit residues: 651.3259 Evaluate side-chains 413 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 4.523 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 236 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 353 optimal weight: 0.9990 chunk 289 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 425 optimal weight: 0.8980 chunk 459 optimal weight: 0.0970 chunk 379 optimal weight: 4.9990 chunk 422 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 341 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 277 ASN E 52 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 HIS ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 HIS J 105 ASN K 52 GLN O 92 HIS ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 277 ASN S 122 ASN U 52 GLN W 122 ASN ** X 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 37476 Z= 0.186 Angle : 0.513 11.797 50628 Z= 0.279 Chirality : 0.037 0.328 5964 Planarity : 0.003 0.031 6444 Dihedral : 3.582 17.179 5172 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.23 (0.11), residues: 4716 helix: 3.05 (0.07), residues: 4368 sheet: None (None), residues: 0 loop : -1.31 (0.33), residues: 348 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 645 time to evaluate : 4.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 650 average time/residue: 0.4873 time to fit residues: 529.5955 Evaluate side-chains 376 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 372 time to evaluate : 4.599 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4106 time to fit residues: 8.8011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 420 optimal weight: 0.9990 chunk 320 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 285 optimal weight: 0.9980 chunk 427 optimal weight: 0.9980 chunk 452 optimal weight: 0.9980 chunk 223 optimal weight: 5.9990 chunk 404 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 ASN ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 GLN K 185 HIS O 52 GLN ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 185 HIS Q 52 GLN S 185 HIS U 52 GLN U 277 ASN ** X 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 37476 Z= 0.196 Angle : 0.499 10.805 50628 Z= 0.274 Chirality : 0.037 0.246 5964 Planarity : 0.003 0.035 6444 Dihedral : 3.596 17.094 5172 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.08 % Favored : 98.71 % Rotamer Outliers : 0.11 % 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: 4.16 (0.11), residues: 4716 helix: 3.02 (0.07), residues: 4380 sheet: None (None), residues: 0 loop : -1.79 (0.33), residues: 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 580 time to evaluate : 4.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 584 average time/residue: 0.4789 time to fit residues: 459.4200 Evaluate side-chains 359 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 356 time to evaluate : 4.638 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3990 time to fit residues: 7.9874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 376 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 336 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 386 optimal weight: 0.9980 chunk 312 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 406 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN E 52 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN G 52 GLN H 36 ASN ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 277 ASN K 52 GLN M 52 GLN M 277 ASN Q 52 GLN S 277 ASN U 52 GLN ** X 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 37476 Z= 0.283 Angle : 0.582 10.351 50628 Z= 0.315 Chirality : 0.038 0.125 5964 Planarity : 0.004 0.047 6444 Dihedral : 3.807 19.132 5172 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.29 % Favored : 98.45 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.11), residues: 4716 helix: 2.76 (0.07), residues: 4380 sheet: None (None), residues: 0 loop : -2.35 (0.32), residues: 336 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 516 time to evaluate : 4.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 522 average time/residue: 0.4727 time to fit residues: 403.8759 Evaluate side-chains 329 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 325 time to evaluate : 4.380 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3690 time to fit residues: 8.4273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 152 optimal weight: 0.6980 chunk 407 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 265 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 452 optimal weight: 3.9990 chunk 375 optimal weight: 0.9990 chunk 209 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 237 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN B 185 HIS B 277 ASN C 52 GLN ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 ASN G 92 HIS ** H 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 HIS ** I 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 GLN ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 92 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.6310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 37476 Z= 0.175 Angle : 0.490 11.765 50628 Z= 0.270 Chirality : 0.036 0.150 5964 Planarity : 0.003 0.044 6444 Dihedral : 3.653 22.798 5172 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.17 % Favored : 98.60 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.11), residues: 4716 helix: 3.06 (0.07), residues: 4380 sheet: None (None), residues: 0 loop : -2.63 (0.31), residues: 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 521 time to evaluate : 4.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 527 average time/residue: 0.4818 time to fit residues: 418.7813 Evaluate side-chains 316 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 313 time to evaluate : 4.398 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3709 time to fit residues: 7.8011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 436 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 257 optimal weight: 0.9990 chunk 330 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 381 optimal weight: 4.9990 chunk 252 optimal weight: 0.7980 chunk 451 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 275 optimal weight: 8.9990 chunk 208 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 277 ASN L 71 ASN M 52 GLN O 52 GLN O 92 HIS ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN U 92 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 37476 Z= 0.202 Angle : 0.517 10.390 50628 Z= 0.283 Chirality : 0.036 0.140 5964 Planarity : 0.003 0.048 6444 Dihedral : 3.678 23.559 5172 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.27 % Favored : 98.49 % Rotamer Outliers : 0.06 % 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: 4.06 (0.11), residues: 4716 helix: 3.05 (0.07), residues: 4356 sheet: None (None), residues: 0 loop : -2.85 (0.28), residues: 360 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 496 time to evaluate : 4.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 498 average time/residue: 0.4848 time to fit residues: 399.9037 Evaluate side-chains 325 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 323 time to evaluate : 4.516 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4006 time to fit residues: 7.2926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 279 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 286 optimal weight: 0.8980 chunk 307 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 354 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN C 52 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** H 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 HIS T 62 GLN ** T 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN W 277 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 37476 Z= 0.251 Angle : 0.565 17.056 50628 Z= 0.306 Chirality : 0.037 0.142 5964 Planarity : 0.004 0.058 6444 Dihedral : 3.739 22.052 5172 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.42 % Favored : 98.32 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.11), residues: 4716 helix: 3.00 (0.07), residues: 4332 sheet: None (None), residues: 0 loop : -2.96 (0.28), residues: 384 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 463 time to evaluate : 4.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 464 average time/residue: 0.4758 time to fit residues: 367.3920 Evaluate side-chains 317 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 316 time to evaluate : 4.732 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3763 time to fit residues: 6.8385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 410 optimal weight: 2.9990 chunk 432 optimal weight: 0.8980 chunk 394 optimal weight: 0.7980 chunk 420 optimal weight: 1.9990 chunk 253 optimal weight: 0.0670 chunk 183 optimal weight: 2.9990 chunk 330 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 379 optimal weight: 0.8980 chunk 397 optimal weight: 0.9980 chunk 418 optimal weight: 4.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN C 52 GLN ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 ASN ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 GLN N 62 GLN ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 216 HIS T 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.6926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 37476 Z= 0.172 Angle : 0.525 15.565 50628 Z= 0.288 Chirality : 0.036 0.160 5964 Planarity : 0.004 0.059 6444 Dihedral : 3.716 25.151 5172 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.40 % Favored : 98.35 % 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: 3.99 (0.12), residues: 4716 helix: 3.03 (0.07), residues: 4356 sheet: None (None), residues: 0 loop : -3.25 (0.29), residues: 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 4.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.4711 time to fit residues: 393.5524 Evaluate side-chains 325 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 4.764 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 276 optimal weight: 5.9990 chunk 444 optimal weight: 1.9990 chunk 271 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 308 optimal weight: 0.3980 chunk 466 optimal weight: 0.9980 chunk 429 optimal weight: 4.9990 chunk 371 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 286 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN C 52 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 HIS ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN M 52 GLN N 62 GLN ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.7080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 37476 Z= 0.185 Angle : 0.533 11.035 50628 Z= 0.294 Chirality : 0.036 0.247 5964 Planarity : 0.004 0.064 6444 Dihedral : 3.726 26.187 5172 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.57 % Favored : 98.18 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.99 (0.11), residues: 4716 helix: 3.06 (0.07), residues: 4332 sheet: None (None), residues: 0 loop : -3.17 (0.28), residues: 384 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 472 time to evaluate : 4.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 473 average time/residue: 0.4689 time to fit residues: 371.5998 Evaluate side-chains 331 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 4.559 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3657 time to fit residues: 6.6474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 294 optimal weight: 0.8980 chunk 395 optimal weight: 0.4980 chunk 113 optimal weight: 4.9990 chunk 342 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 371 optimal weight: 0.5980 chunk 155 optimal weight: 0.6980 chunk 381 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN G 52 GLN H 62 GLN L 62 GLN ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 62 GLN U 92 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.066053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.052013 restraints weight = 166760.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.053148 restraints weight = 124739.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.053918 restraints weight = 102476.855| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.7240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 37476 Z= 0.181 Angle : 0.534 11.848 50628 Z= 0.294 Chirality : 0.036 0.208 5964 Planarity : 0.004 0.051 6444 Dihedral : 3.758 24.678 5172 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.78 % Favored : 97.99 % 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: 3.96 (0.12), residues: 4716 helix: 3.04 (0.07), residues: 4332 sheet: None (None), residues: 0 loop : -3.19 (0.28), residues: 384 =============================================================================== Job complete usr+sys time: 8437.02 seconds wall clock time: 153 minutes 56.36 seconds (9236.36 seconds total)