Starting phenix.real_space_refine on Wed Sep 25 15:29:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixl_35795/09_2024/8ixl_35795.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixl_35795/09_2024/8ixl_35795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixl_35795/09_2024/8ixl_35795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixl_35795/09_2024/8ixl_35795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixl_35795/09_2024/8ixl_35795.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixl_35795/09_2024/8ixl_35795.cif" } resolution = 3.5 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= 0.000 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 7220 2.51 5 N 1720 2.21 5 O 1980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10970 Number of models: 1 Model: "" Number of chains: 35 Chain: "Z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "B" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "C" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "D" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 256 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "E" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "F" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "H" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "A" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "G" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "I" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "J" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 256 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "K" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "L" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "M" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "N" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "O" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Q" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 256 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "R" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "S" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "T" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "V" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "W" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "X" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Y" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 256 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "AA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BA" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "CA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "FA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "GA" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 256 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "HA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "IA" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "JA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Time building chain proxies: 8.07, per 1000 atoms: 0.74 Number of scatterers: 10970 At special positions: 0 Unit cell: (74.69, 76.63, 155.2, 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 50 16.00 O 1980 8.00 N 1720 7.00 C 7220 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 - 3.00 Amino acid : True - 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: 2.91 Conformation dependent library (CDL) restraints added in 1.2 seconds 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2710 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 0 sheets defined 96.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'Z' and resid 5 through 50 removed outlier: 3.954A pdb=" N VAL Z 31 " --> pdb=" O ALA Z 27 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY Z 38 " --> pdb=" O GLY Z 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 50 Processing helix chain 'C' and resid 6 through 50 Processing helix chain 'D' and resid 2 through 32 removed outlier: 3.947A pdb=" N ILE D 21 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 49 removed outlier: 3.745A pdb=" N GLU E 20 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 31 Processing helix chain 'H' and resid 6 through 50 Processing helix chain 'A' and resid 6 through 50 removed outlier: 3.954A pdb=" N VAL A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 50 Processing helix chain 'I' and resid 6 through 50 Processing helix chain 'J' and resid 2 through 32 removed outlier: 3.947A pdb=" N ILE J 21 " --> pdb=" O LEU J 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 49 removed outlier: 3.745A pdb=" N GLU K 20 " --> pdb=" O ALA K 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 31 Processing helix chain 'M' and resid 6 through 50 Processing helix chain 'N' and resid 6 through 50 removed outlier: 3.954A pdb=" N VAL N 31 " --> pdb=" O ALA N 27 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY N 38 " --> pdb=" O GLY N 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 50 Processing helix chain 'P' and resid 6 through 50 Processing helix chain 'Q' and resid 2 through 32 removed outlier: 3.947A pdb=" N ILE Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 49 removed outlier: 3.745A pdb=" N GLU R 20 " --> pdb=" O ALA R 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 31 Processing helix chain 'T' and resid 6 through 50 Processing helix chain 'V' and resid 6 through 50 removed outlier: 3.954A pdb=" N VAL V 31 " --> pdb=" O ALA V 27 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY V 38 " --> pdb=" O GLY V 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 50 Processing helix chain 'X' and resid 6 through 50 Processing helix chain 'Y' and resid 2 through 32 removed outlier: 3.947A pdb=" N ILE Y 21 " --> pdb=" O LEU Y 17 " (cutoff:3.500A) Processing helix chain 'AA' and resid 7 through 49 removed outlier: 3.745A pdb=" N GLUAA 20 " --> pdb=" O ALAAA 16 " (cutoff:3.500A) Processing helix chain 'BA' and resid 6 through 31 Processing helix chain 'CA' and resid 6 through 50 Processing helix chain 'DA' and resid 6 through 50 removed outlier: 3.954A pdb=" N VALDA 31 " --> pdb=" O ALADA 27 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLYDA 38 " --> pdb=" O GLYDA 34 " (cutoff:3.500A) Processing helix chain 'EA' and resid 6 through 50 Processing helix chain 'FA' and resid 6 through 50 Processing helix chain 'GA' and resid 2 through 32 removed outlier: 3.947A pdb=" N ILEGA 21 " --> pdb=" O LEUGA 17 " (cutoff:3.500A) Processing helix chain 'HA' and resid 7 through 49 removed outlier: 3.745A pdb=" N GLUHA 20 " --> pdb=" O ALAHA 16 " (cutoff:3.500A) Processing helix chain 'IA' and resid 6 through 31 Processing helix chain 'JA' and resid 6 through 50 1241 hydrogen bonds defined for protein. 3723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1998 1.33 - 1.45: 2802 1.45 - 1.57: 6295 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 11185 Sorted by residual: bond pdb=" N VALHA 31 " pdb=" CA VALHA 31 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.38e+00 bond pdb=" N VAL R 31 " pdb=" CA VAL R 31 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.35e+00 bond pdb=" N VAL A 31 " pdb=" CA VAL A 31 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.27e+00 bond pdb=" N VAL Z 31 " pdb=" CA VAL Z 31 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.27e+00 bond pdb=" N VAL V 31 " pdb=" CA VAL V 31 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.26e+00 ... (remaining 11180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 9981 1.37 - 2.74: 4273 2.74 - 4.12: 827 4.12 - 5.49: 18 5.49 - 6.86: 31 Bond angle restraints: 15130 Sorted by residual: angle pdb=" N ALA Z 49 " pdb=" CA ALA Z 49 " pdb=" C ALA Z 49 " ideal model delta sigma weight residual 111.28 105.79 5.49 1.09e+00 8.42e-01 2.54e+01 angle pdb=" N ALADA 49 " pdb=" CA ALADA 49 " pdb=" C ALADA 49 " ideal model delta sigma weight residual 111.28 105.80 5.48 1.09e+00 8.42e-01 2.53e+01 angle pdb=" N ALA N 49 " pdb=" CA ALA N 49 " pdb=" C ALA N 49 " ideal model delta sigma weight residual 111.28 105.80 5.48 1.09e+00 8.42e-01 2.53e+01 angle pdb=" N ALA A 49 " pdb=" CA ALA A 49 " pdb=" C ALA A 49 " ideal model delta sigma weight residual 111.28 105.81 5.47 1.09e+00 8.42e-01 2.52e+01 angle pdb=" N ALA V 49 " pdb=" CA ALA V 49 " pdb=" C ALA V 49 " ideal model delta sigma weight residual 111.28 105.82 5.46 1.09e+00 8.42e-01 2.51e+01 ... (remaining 15125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 6095 16.39 - 32.78: 305 32.78 - 49.16: 80 49.16 - 65.55: 15 65.55 - 81.94: 10 Dihedral angle restraints: 6505 sinusoidal: 2310 harmonic: 4195 Sorted by residual: dihedral pdb=" CA LEU A 14 " pdb=" CB LEU A 14 " pdb=" CG LEU A 14 " pdb=" CD1 LEU A 14 " ideal model delta sinusoidal sigma weight residual 180.00 130.13 49.87 3 1.50e+01 4.44e-03 8.83e+00 dihedral pdb=" CA LEU N 14 " pdb=" CB LEU N 14 " pdb=" CG LEU N 14 " pdb=" CD1 LEU N 14 " ideal model delta sinusoidal sigma weight residual 180.00 130.14 49.86 3 1.50e+01 4.44e-03 8.83e+00 dihedral pdb=" CA LEU V 14 " pdb=" CB LEU V 14 " pdb=" CG LEU V 14 " pdb=" CD1 LEU V 14 " ideal model delta sinusoidal sigma weight residual 180.00 130.14 49.86 3 1.50e+01 4.44e-03 8.83e+00 ... (remaining 6502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 391 0.041 - 0.082: 488 0.082 - 0.122: 508 0.122 - 0.163: 309 0.163 - 0.204: 89 Chirality restraints: 1785 Sorted by residual: chirality pdb=" CA ILE Y 21 " pdb=" N ILE Y 21 " pdb=" C ILE Y 21 " pdb=" CB ILE Y 21 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE Q 21 " pdb=" N ILE Q 21 " pdb=" C ILE Q 21 " pdb=" CB ILE Q 21 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILEGA 21 " pdb=" N ILEGA 21 " pdb=" C ILEGA 21 " pdb=" CB ILEGA 21 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1782 not shown) Planarity restraints: 1820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLUCA 20 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.29e+00 pdb=" C GLUCA 20 " 0.020 2.00e-02 2.50e+03 pdb=" O GLUCA 20 " -0.007 2.00e-02 2.50e+03 pdb=" N TYRCA 21 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLUJA 20 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C GLUJA 20 " -0.020 2.00e-02 2.50e+03 pdb=" O GLUJA 20 " 0.007 2.00e-02 2.50e+03 pdb=" N TYRJA 21 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU T 20 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C GLU T 20 " 0.020 2.00e-02 2.50e+03 pdb=" O GLU T 20 " -0.007 2.00e-02 2.50e+03 pdb=" N TYR T 21 " -0.007 2.00e-02 2.50e+03 ... (remaining 1817 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.03: 7191 3.03 - 3.50: 12629 3.50 - 3.97: 17550 3.97 - 4.43: 19850 4.43 - 4.90: 31840 Nonbonded interactions: 89060 Sorted by model distance: nonbonded pdb=" O SER A 50 " pdb=" OG SER A 50 " model vdw 2.568 3.040 nonbonded pdb=" O SER V 50 " pdb=" OG SER V 50 " model vdw 2.569 3.040 nonbonded pdb=" O SER Z 50 " pdb=" OG SER Z 50 " model vdw 2.569 3.040 nonbonded pdb=" O SERDA 50 " pdb=" OG SERDA 50 " model vdw 2.569 3.040 nonbonded pdb=" O SER N 50 " pdb=" OG SER N 50 " model vdw 2.570 3.040 ... (remaining 89055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'AA' selection = chain 'B' selection = chain 'C' selection = chain 'CA' selection = chain 'DA' selection = chain 'E' selection = chain 'EA' selection = chain 'FA' selection = chain 'G' selection = chain 'H' selection = chain 'HA' selection = chain 'I' selection = chain 'JA' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'BA' selection = chain 'F' selection = chain 'IA' selection = chain 'L' selection = chain 'S' } ncs_group { reference = chain 'D' selection = chain 'GA' selection = chain 'J' selection = chain 'Q' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.430 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.012 0.039 11185 Z= 0.784 Angle : 1.477 6.862 15130 Z= 1.242 Chirality : 0.095 0.204 1785 Planarity : 0.003 0.011 1820 Dihedral : 11.647 81.940 3795 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % 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: 2.40 (0.19), residues: 1385 helix: 1.64 (0.12), residues: 1380 sheet: None (None), residues: 0 loop : -0.15 (0.01), residues: 5 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Q 15 PHE 0.013 0.002 PHEIA 7 TYR 0.010 0.002 TYR G 24 ARG 0.001 0.000 ARG J 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 1.154 Fit side-chains REVERT: H 43 LYS cc_start: 0.8687 (ttmt) cc_final: 0.8479 (mtmt) REVERT: M 24 TYR cc_start: 0.8055 (m-10) cc_final: 0.7593 (m-10) REVERT: Q 28 MET cc_start: 0.7656 (mmt) cc_final: 0.7366 (mmp) REVERT: R 11 PHE cc_start: 0.7761 (t80) cc_final: 0.7500 (t80) REVERT: CA 43 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8207 (mtmt) REVERT: JA 24 TYR cc_start: 0.7995 (m-10) cc_final: 0.7623 (m-10) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.2991 time to fit residues: 127.3715 Evaluate side-chains 246 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 15 GLN L 32 GLN P 15 GLN AA 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11185 Z= 0.181 Angle : 0.414 6.330 15130 Z= 0.248 Chirality : 0.035 0.107 1785 Planarity : 0.003 0.019 1820 Dihedral : 7.638 81.982 1535 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.26 % Allowed : 10.86 % Favored : 86.88 % 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: 5.20 (0.18), residues: 1385 helix: 3.45 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.05 (0.35), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPFA 26 PHE 0.024 0.001 PHEAA 11 TYR 0.022 0.001 TYRFA 21 ARG 0.001 0.000 ARG S 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 325 time to evaluate : 1.223 Fit side-chains REVERT: B 44 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8583 (ttpt) REVERT: E 24 TYR cc_start: 0.7956 (m-10) cc_final: 0.7743 (m-10) REVERT: G 44 LYS cc_start: 0.8884 (ttmt) cc_final: 0.8600 (tttp) REVERT: K 24 TYR cc_start: 0.7992 (m-10) cc_final: 0.7751 (m-10) REVERT: R 24 TYR cc_start: 0.8071 (m-10) cc_final: 0.7832 (m-10) REVERT: S 18 SER cc_start: 0.9069 (t) cc_final: 0.8856 (m) REVERT: W 44 LYS cc_start: 0.9000 (ttmt) cc_final: 0.8732 (ttmt) REVERT: HA 24 TYR cc_start: 0.7980 (m-10) cc_final: 0.7761 (m-10) REVERT: JA 43 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8301 (mtmt) outliers start: 25 outliers final: 10 residues processed: 341 average time/residue: 0.2383 time to fit residues: 111.6402 Evaluate side-chains 299 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 288 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain DA residue 31 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 11185 Z= 0.167 Angle : 0.379 4.598 15130 Z= 0.226 Chirality : 0.034 0.121 1785 Planarity : 0.002 0.018 1820 Dihedral : 7.246 84.706 1535 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 1.27 % Allowed : 16.92 % Favored : 81.81 % 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: 5.76 (0.18), residues: 1385 helix: 3.77 (0.11), residues: 1350 sheet: None (None), residues: 0 loop : 1.02 (0.30), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPFA 26 PHE 0.015 0.001 PHEAA 11 TYR 0.012 0.001 TYR M 24 ARG 0.001 0.000 ARG Q 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 299 time to evaluate : 1.246 Fit side-chains REVERT: G 44 LYS cc_start: 0.8922 (ttmt) cc_final: 0.8656 (tttp) REVERT: O 41 LEU cc_start: 0.9348 (mt) cc_final: 0.9134 (mt) REVERT: R 28 MET cc_start: 0.7606 (ttp) cc_final: 0.7347 (ttp) REVERT: T 40 LYS cc_start: 0.8737 (tttt) cc_final: 0.8501 (tttt) REVERT: CA 40 LYS cc_start: 0.8634 (tttt) cc_final: 0.8395 (tttt) REVERT: JA 40 LYS cc_start: 0.8484 (tttt) cc_final: 0.8178 (tttt) outliers start: 14 outliers final: 8 residues processed: 304 average time/residue: 0.2370 time to fit residues: 99.4011 Evaluate side-chains 292 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 284 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain HA residue 46 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 11185 Z= 0.164 Angle : 0.368 4.369 15130 Z= 0.221 Chirality : 0.034 0.123 1785 Planarity : 0.002 0.018 1820 Dihedral : 6.899 89.396 1535 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.99 % Allowed : 17.92 % Favored : 80.09 % 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: 5.80 (0.18), residues: 1385 helix: 3.79 (0.11), residues: 1350 sheet: None (None), residues: 0 loop : 1.32 (0.36), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 26 PHE 0.019 0.001 PHE E 11 TYR 0.012 0.001 TYR T 24 ARG 0.001 0.000 ARG S 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 303 time to evaluate : 1.187 Fit side-chains REVERT: M 40 LYS cc_start: 0.8654 (tttt) cc_final: 0.8451 (tttt) REVERT: T 40 LYS cc_start: 0.8647 (tttt) cc_final: 0.8411 (tttt) REVERT: BA 18 SER cc_start: 0.8886 (t) cc_final: 0.8680 (m) REVERT: CA 40 LYS cc_start: 0.8525 (tttt) cc_final: 0.8263 (tttt) REVERT: DA 22 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8210 (tp) REVERT: JA 40 LYS cc_start: 0.8451 (tttt) cc_final: 0.8092 (tttt) outliers start: 22 outliers final: 17 residues processed: 314 average time/residue: 0.2343 time to fit residues: 101.8794 Evaluate side-chains 305 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 287 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 48 LYS Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain AA residue 36 THR Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain DA residue 22 ILE Chi-restraints excluded: chain DA residue 44 LYS Chi-restraints excluded: chain GA residue 1 MET Chi-restraints excluded: chain HA residue 46 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11185 Z= 0.277 Angle : 0.439 5.746 15130 Z= 0.259 Chirality : 0.036 0.124 1785 Planarity : 0.003 0.022 1820 Dihedral : 6.909 89.225 1535 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 4.16 % Allowed : 18.19 % Favored : 77.65 % 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: 5.51 (0.19), residues: 1385 helix: 3.63 (0.12), residues: 1350 sheet: None (None), residues: 0 loop : 0.42 (0.53), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPFA 26 PHE 0.021 0.002 PHE K 11 TYR 0.014 0.001 TYR K 24 ARG 0.001 0.000 ARG S 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 286 time to evaluate : 1.183 Fit side-chains REVERT: A 22 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8394 (tp) REVERT: K 11 PHE cc_start: 0.7581 (t80) cc_final: 0.7376 (t80) REVERT: N 22 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8508 (tp) REVERT: S 18 SER cc_start: 0.9104 (t) cc_final: 0.8892 (m) REVERT: T 40 LYS cc_start: 0.8650 (tttt) cc_final: 0.8385 (tttt) REVERT: AA 11 PHE cc_start: 0.7177 (t80) cc_final: 0.6603 (t80) REVERT: CA 40 LYS cc_start: 0.8542 (tttt) cc_final: 0.8328 (tttt) REVERT: DA 22 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8249 (tp) REVERT: JA 40 LYS cc_start: 0.8476 (tttt) cc_final: 0.8072 (tttt) outliers start: 46 outliers final: 32 residues processed: 315 average time/residue: 0.2331 time to fit residues: 101.0997 Evaluate side-chains 312 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 277 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 48 LYS Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 30 VAL Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain AA residue 36 THR Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain DA residue 22 ILE Chi-restraints excluded: chain DA residue 31 VAL Chi-restraints excluded: chain DA residue 44 LYS Chi-restraints excluded: chain GA residue 1 MET Chi-restraints excluded: chain GA residue 31 SER Chi-restraints excluded: chain HA residue 36 THR Chi-restraints excluded: chain HA residue 46 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.0570 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11185 Z= 0.166 Angle : 0.392 6.031 15130 Z= 0.230 Chirality : 0.035 0.127 1785 Planarity : 0.003 0.024 1820 Dihedral : 6.637 89.012 1535 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.35 % Allowed : 20.09 % Favored : 77.56 % 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: 5.72 (0.18), residues: 1385 helix: 3.77 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.53 (0.47), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 26 PHE 0.022 0.001 PHE R 11 TYR 0.016 0.001 TYRJA 24 ARG 0.001 0.000 ARG J 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 299 time to evaluate : 1.576 Fit side-chains REVERT: C 21 TYR cc_start: 0.8493 (m-80) cc_final: 0.8253 (m-80) REVERT: H 40 LYS cc_start: 0.8866 (tttt) cc_final: 0.8664 (tttt) REVERT: A 22 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8151 (tp) REVERT: N 22 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8502 (tp) REVERT: AA 24 TYR cc_start: 0.7829 (m-10) cc_final: 0.7608 (m-10) REVERT: JA 40 LYS cc_start: 0.8460 (tttt) cc_final: 0.7998 (tttt) outliers start: 26 outliers final: 21 residues processed: 314 average time/residue: 0.2246 time to fit residues: 98.4533 Evaluate side-chains 310 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 287 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain AA residue 36 THR Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain CA residue 20 GLU Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain DA residue 31 VAL Chi-restraints excluded: chain GA residue 1 MET Chi-restraints excluded: chain HA residue 36 THR Chi-restraints excluded: chain HA residue 46 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11185 Z= 0.173 Angle : 0.407 7.120 15130 Z= 0.237 Chirality : 0.035 0.145 1785 Planarity : 0.003 0.023 1820 Dihedral : 6.550 88.880 1535 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 2.71 % Allowed : 20.45 % Favored : 76.83 % 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: 5.77 (0.18), residues: 1385 helix: 3.80 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.58 (0.47), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 26 PHE 0.025 0.001 PHEAA 11 TYR 0.016 0.001 TYRCA 24 ARG 0.001 0.000 ARG Q 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 298 time to evaluate : 1.288 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8038 (tp) REVERT: H 40 LYS cc_start: 0.8828 (tttt) cc_final: 0.8621 (tttt) REVERT: A 22 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8202 (tp) REVERT: N 22 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8430 (tp) REVERT: AA 11 PHE cc_start: 0.7374 (t80) cc_final: 0.7129 (t80) REVERT: CA 40 LYS cc_start: 0.8515 (tttt) cc_final: 0.8272 (tttt) REVERT: DA 22 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8208 (tp) REVERT: JA 40 LYS cc_start: 0.8425 (tttt) cc_final: 0.7954 (tttt) outliers start: 30 outliers final: 24 residues processed: 314 average time/residue: 0.2431 time to fit residues: 107.7765 Evaluate side-chains 319 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 291 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain AA residue 36 THR Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain CA residue 20 GLU Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain DA residue 22 ILE Chi-restraints excluded: chain DA residue 31 VAL Chi-restraints excluded: chain DA residue 44 LYS Chi-restraints excluded: chain GA residue 1 MET Chi-restraints excluded: chain HA residue 46 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: HA 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11185 Z= 0.183 Angle : 0.414 6.733 15130 Z= 0.240 Chirality : 0.035 0.134 1785 Planarity : 0.003 0.022 1820 Dihedral : 6.489 88.181 1535 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.35 % Allowed : 20.54 % Favored : 76.11 % 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: 5.74 (0.18), residues: 1385 helix: 3.78 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.57 (0.46), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 26 PHE 0.031 0.001 PHE E 11 TYR 0.019 0.001 TYRCA 21 ARG 0.001 0.000 ARG Q 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 299 time to evaluate : 1.198 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8026 (tp) REVERT: H 40 LYS cc_start: 0.8788 (tttt) cc_final: 0.8559 (tttt) REVERT: A 22 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8062 (tp) REVERT: N 22 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8364 (tp) REVERT: AA 11 PHE cc_start: 0.7391 (t80) cc_final: 0.7185 (t80) REVERT: CA 40 LYS cc_start: 0.8502 (tttt) cc_final: 0.8248 (tttt) REVERT: DA 22 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8214 (tp) REVERT: JA 40 LYS cc_start: 0.8462 (tttt) cc_final: 0.8023 (tttt) outliers start: 37 outliers final: 30 residues processed: 318 average time/residue: 0.2216 time to fit residues: 98.7832 Evaluate side-chains 328 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 294 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain S residue 15 ILE Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain AA residue 36 THR Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain CA residue 37 ILE Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain DA residue 22 ILE Chi-restraints excluded: chain DA residue 29 VAL Chi-restraints excluded: chain DA residue 31 VAL Chi-restraints excluded: chain DA residue 44 LYS Chi-restraints excluded: chain GA residue 1 MET Chi-restraints excluded: chain HA residue 36 THR Chi-restraints excluded: chain HA residue 46 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11185 Z= 0.187 Angle : 0.430 6.521 15130 Z= 0.249 Chirality : 0.036 0.151 1785 Planarity : 0.003 0.022 1820 Dihedral : 6.456 88.329 1535 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.26 % Allowed : 20.63 % Favored : 76.11 % 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: 5.67 (0.18), residues: 1385 helix: 3.74 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.51 (0.45), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP W 26 PHE 0.026 0.001 PHE R 11 TYR 0.022 0.001 TYRCA 24 ARG 0.001 0.000 ARG Q 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 297 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: Z 22 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.7998 (tp) REVERT: A 22 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8039 (tp) REVERT: N 22 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8488 (tp) REVERT: DA 22 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8190 (tp) REVERT: JA 40 LYS cc_start: 0.8460 (tttt) cc_final: 0.8009 (tttt) outliers start: 36 outliers final: 30 residues processed: 314 average time/residue: 0.2205 time to fit residues: 97.4356 Evaluate side-chains 328 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 294 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain S residue 15 ILE Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain AA residue 36 THR Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain CA residue 20 GLU Chi-restraints excluded: chain CA residue 37 ILE Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain DA residue 22 ILE Chi-restraints excluded: chain DA residue 29 VAL Chi-restraints excluded: chain DA residue 31 VAL Chi-restraints excluded: chain DA residue 44 LYS Chi-restraints excluded: chain GA residue 1 MET Chi-restraints excluded: chain HA residue 36 THR Chi-restraints excluded: chain HA residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 124 optimal weight: 0.0970 chunk 114 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 11185 Z= 0.185 Angle : 0.441 6.923 15130 Z= 0.255 Chirality : 0.036 0.181 1785 Planarity : 0.003 0.023 1820 Dihedral : 6.432 88.201 1535 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.08 % Allowed : 21.36 % Favored : 75.57 % 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: 5.63 (0.18), residues: 1385 helix: 3.71 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.60 (0.45), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP W 26 PHE 0.025 0.001 PHEAA 11 TYR 0.035 0.001 TYR T 24 ARG 0.001 0.000 ARG S 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 307 time to evaluate : 1.435 Fit side-chains revert: symmetry clash REVERT: Z 22 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.7994 (tp) REVERT: A 22 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8013 (tp) REVERT: M 20 GLU cc_start: 0.6706 (tt0) cc_final: 0.6328 (tt0) REVERT: T 24 TYR cc_start: 0.8190 (m-80) cc_final: 0.7958 (m-80) REVERT: X 21 TYR cc_start: 0.8526 (m-80) cc_final: 0.8293 (m-80) REVERT: DA 22 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8130 (tp) REVERT: JA 40 LYS cc_start: 0.8446 (tttt) cc_final: 0.7971 (tttt) outliers start: 34 outliers final: 28 residues processed: 323 average time/residue: 0.2243 time to fit residues: 101.0190 Evaluate side-chains 328 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 297 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain S residue 15 ILE Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 47 SER Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain AA residue 36 THR Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain CA residue 20 GLU Chi-restraints excluded: chain CA residue 37 ILE Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain DA residue 22 ILE Chi-restraints excluded: chain DA residue 29 VAL Chi-restraints excluded: chain DA residue 31 VAL Chi-restraints excluded: chain DA residue 44 LYS Chi-restraints excluded: chain GA residue 1 MET Chi-restraints excluded: chain HA residue 36 THR Chi-restraints excluded: chain HA residue 46 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.097833 restraints weight = 17034.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101249 restraints weight = 9005.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.103600 restraints weight = 5816.686| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 11185 Z= 0.186 Angle : 0.449 8.691 15130 Z= 0.258 Chirality : 0.036 0.162 1785 Planarity : 0.003 0.021 1820 Dihedral : 6.377 87.892 1535 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.99 % Allowed : 21.18 % Favored : 75.84 % 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: 5.61 (0.18), residues: 1385 helix: 3.69 (0.12), residues: 1345 sheet: None (None), residues: 0 loop : 0.71 (0.47), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP W 26 PHE 0.026 0.001 PHEAA 11 TYR 0.033 0.001 TYR T 24 ARG 0.001 0.000 ARG S 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2338.38 seconds wall clock time: 42 minutes 43.90 seconds (2563.90 seconds total)