Starting phenix.real_space_refine on Sat Dec 9 11:17:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixl_35795/12_2023/8ixl_35795.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixl_35795/12_2023/8ixl_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_35795/12_2023/8ixl_35795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixl_35795/12_2023/8ixl_35795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixl_35795/12_2023/8ixl_35795.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixl_35795/12_2023/8ixl_35795.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 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: 6.05, per 1000 atoms: 0.55 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 - 3.50 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: 4.32 Conformation dependent library (CDL) restraints added in 2.0 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: 0.91 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: 3.63 Time building geometry restraints manager: 4.63 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: 100.18 - 107.04: 201 107.04 - 113.90: 6375 113.90 - 120.76: 4906 120.76 - 127.62: 3588 127.62 - 134.48: 60 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 2.440 nonbonded pdb=" O SER V 50 " pdb=" OG SER V 50 " model vdw 2.569 2.440 nonbonded pdb=" O SER Z 50 " pdb=" OG SER Z 50 " model vdw 2.569 2.440 nonbonded pdb=" O SERDA 50 " pdb=" OG SERDA 50 " model vdw 2.569 2.440 nonbonded pdb=" O SER N 50 " pdb=" OG SER N 50 " model vdw 2.570 2.440 ... (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 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.490 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 31.450 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.130 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.870 ------------------------------------------------------------------------------- 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 : 1.403 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.3070 time to fit residues: 130.6584 Evaluate side-chains 246 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5503 ------------------------------------------------------------------------------- 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: 2.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 12 ASN I 15 GLN L 32 GLN P 15 GLN R 12 ASN AA 12 ASN AA 15 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11185 Z= 0.170 Angle : 0.410 6.493 15130 Z= 0.243 Chirality : 0.035 0.108 1785 Planarity : 0.003 0.022 1820 Dihedral : 7.545 79.740 1535 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.81 % Allowed : 10.50 % Favored : 86.70 % 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: 5.19 (0.18), residues: 1385 helix: 3.44 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.00 (0.30), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPEA 26 PHE 0.025 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 372 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 341 time to evaluate : 1.246 Fit side-chains outliers start: 31 outliers final: 13 residues processed: 359 average time/residue: 0.2486 time to fit residues: 121.9765 Evaluate side-chains 317 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 304 time to evaluate : 1.321 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1236 time to fit residues: 4.3276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8280 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 11185 Z= 0.157 Angle : 0.370 4.891 15130 Z= 0.220 Chirality : 0.033 0.119 1785 Planarity : 0.002 0.019 1820 Dihedral : 6.915 81.706 1535 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 1.27 % Allowed : 16.65 % Favored : 82.08 % 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: 5.86 (0.18), residues: 1385 helix: 3.83 (0.11), residues: 1350 sheet: None (None), residues: 0 loop : 1.11 (0.30), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPFA 26 PHE 0.013 0.001 PHEAA 11 TYR 0.011 0.001 TYR M 24 ARG 0.001 0.000 ARG D 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 320 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 306 time to evaluate : 1.179 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 312 average time/residue: 0.2490 time to fit residues: 106.5309 Evaluate side-chains 296 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 290 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1571 time to fit residues: 3.1621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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: 0.8347 moved from start: 0.3688 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= 0.210 Angle : 0.397 4.331 15130 Z= 0.236 Chirality : 0.035 0.118 1785 Planarity : 0.003 0.021 1820 Dihedral : 6.702 87.526 1535 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.26 % Allowed : 17.29 % Favored : 80.45 % 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: 5.71 (0.19), residues: 1385 helix: 3.75 (0.12), residues: 1350 sheet: None (None), residues: 0 loop : 0.78 (0.39), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPFA 26 PHE 0.025 0.001 PHEAA 11 TYR 0.015 0.001 TYRJA 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 315 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 290 time to evaluate : 1.276 Fit side-chains outliers start: 25 outliers final: 17 residues processed: 305 average time/residue: 0.2439 time to fit residues: 102.7298 Evaluate side-chains 296 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 279 time to evaluate : 1.271 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1533 time to fit residues: 5.7162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.3974 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 : 0.391 7.803 15130 Z= 0.227 Chirality : 0.034 0.122 1785 Planarity : 0.002 0.023 1820 Dihedral : 6.427 81.234 1535 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 1.00 % Allowed : 18.10 % Favored : 80.90 % 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: 5.86 (0.18), residues: 1385 helix: 3.86 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.53 (0.44), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 26 PHE 0.020 0.001 PHE K 11 TYR 0.022 0.001 TYR T 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 311 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 300 time to evaluate : 1.287 Fit side-chains outliers start: 11 outliers final: 11 residues processed: 305 average time/residue: 0.2371 time to fit residues: 100.5344 Evaluate side-chains 297 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 286 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0907 time to fit residues: 3.3831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.8353 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11185 Z= 0.216 Angle : 0.410 6.409 15130 Z= 0.240 Chirality : 0.035 0.121 1785 Planarity : 0.003 0.024 1820 Dihedral : 6.313 81.405 1535 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.36 % Allowed : 19.37 % Favored : 79.28 % 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 (0.19), residues: 1385 helix: 3.79 (0.12), residues: 1345 sheet: None (None), residues: 0 loop : 0.25 (0.50), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 26 PHE 0.030 0.001 PHE E 11 TYR 0.020 0.001 TYRJA 24 ARG 0.001 0.000 ARG S 33 *********************** 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 306 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 291 time to evaluate : 1.234 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 296 average time/residue: 0.2398 time to fit residues: 98.5796 Evaluate side-chains 294 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 285 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1026 time to fit residues: 3.3145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 88 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 15 GLN HA 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11185 Z= 0.159 Angle : 0.394 6.619 15130 Z= 0.229 Chirality : 0.034 0.123 1785 Planarity : 0.003 0.025 1820 Dihedral : 6.053 77.858 1535 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 0.36 % Allowed : 20.27 % Favored : 79.37 % 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: 5.85 (0.18), residues: 1385 helix: 3.85 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.70 (0.49), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 26 PHE 0.022 0.001 PHEAA 11 TYR 0.015 0.001 TYRAA 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 314 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 310 time to evaluate : 1.318 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 310 average time/residue: 0.2448 time to fit residues: 106.6950 Evaluate side-chains 300 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 297 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1059 time to fit residues: 2.1873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 94 optimal weight: 0.2980 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.8336 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11185 Z= 0.206 Angle : 0.419 7.073 15130 Z= 0.243 Chirality : 0.035 0.118 1785 Planarity : 0.003 0.025 1820 Dihedral : 6.078 77.234 1535 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 0.90 % Allowed : 20.72 % Favored : 78.37 % 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: 5.71 (0.19), residues: 1385 helix: 3.77 (0.12), residues: 1345 sheet: None (None), residues: 0 loop : 0.42 (0.50), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 26 PHE 0.018 0.001 PHEAA 11 TYR 0.027 0.002 TYRJA 24 ARG 0.001 0.000 ARG S 33 *********************** 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 307 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 297 time to evaluate : 1.234 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 299 average time/residue: 0.2357 time to fit residues: 98.1278 Evaluate side-chains 299 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 290 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1017 time to fit residues: 3.3291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8304 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11185 Z= 0.181 Angle : 0.420 7.089 15130 Z= 0.242 Chirality : 0.035 0.143 1785 Planarity : 0.003 0.024 1820 Dihedral : 6.000 76.240 1535 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 0.54 % Allowed : 21.09 % Favored : 78.37 % 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 (0.19), residues: 1385 helix: 3.78 (0.12), residues: 1345 sheet: None (None), residues: 0 loop : 0.57 (0.48), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP W 26 PHE 0.020 0.001 PHEHA 11 TYR 0.025 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 308 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 302 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 304 average time/residue: 0.2372 time to fit residues: 100.6471 Evaluate side-chains 299 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 296 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0985 time to fit residues: 2.2405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8306 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11185 Z= 0.187 Angle : 0.433 7.336 15130 Z= 0.248 Chirality : 0.036 0.151 1785 Planarity : 0.003 0.024 1820 Dihedral : 6.016 76.643 1535 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.00 % Allowed : 21.99 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.72 (0.19), residues: 1385 helix: 3.77 (0.12), residues: 1345 sheet: None (None), residues: 0 loop : 0.55 (0.48), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP W 26 PHE 0.026 0.001 PHEHA 11 TYR 0.029 0.001 TYRJA 24 ARG 0.001 0.000 ARG Q 26 ********************** 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 301 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 1.489 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.2413 time to fit residues: 101.4724 Evaluate side-chains 297 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.113093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096352 restraints weight = 17120.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.099697 restraints weight = 9050.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.102023 restraints weight = 5852.370| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11185 Z= 0.190 Angle : 0.445 8.352 15130 Z= 0.255 Chirality : 0.036 0.182 1785 Planarity : 0.003 0.023 1820 Dihedral : 5.983 76.202 1535 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.54 % Allowed : 21.45 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.68 (0.19), residues: 1385 helix: 3.75 (0.12), residues: 1345 sheet: None (None), residues: 0 loop : 0.52 (0.48), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP W 26 PHE 0.022 0.001 PHE K 11 TYR 0.031 0.001 TYRCA 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: 2402.08 seconds wall clock time: 44 minutes 38.00 seconds (2678.00 seconds total)