Starting phenix.real_space_refine on Fri Mar 15 06:49:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixl_35795/03_2024/8ixl_35795.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixl_35795/03_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_35795/03_2024/8ixl_35795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixl_35795/03_2024/8ixl_35795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixl_35795/03_2024/8ixl_35795.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixl_35795/03_2024/8ixl_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-dev-5265/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: 6.10, per 1000 atoms: 0.56 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: 4.33 Conformation dependent library (CDL) restraints added in 2.1 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: 0.90 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: 3.58 Time building geometry restraints manager: 4.72 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: 0.570 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: 3.420 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.390 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.140 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.550 ------------------------------------------------------------------------------- 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 : 1.320 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: 0.2933 time to fit residues: 124.6250 Evaluate side-chains 246 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3048 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= 0.174 Angle : 0.406 6.522 15130 Z= 0.242 Chirality : 0.035 0.108 1785 Planarity : 0.003 0.020 1820 Dihedral : 7.643 80.391 1535 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.71 % Allowed : 10.41 % 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: 5.23 (0.18), residues: 1385 helix: 3.47 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : -0.11 (0.31), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPFA 26 PHE 0.026 0.001 PHEAA 11 TYR 0.023 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 356 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 326 time to evaluate : 1.160 Fit side-chains REVERT: B 44 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8501 (ttpt) REVERT: G 44 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8604 (tttp) REVERT: K 24 TYR cc_start: 0.7944 (m-10) cc_final: 0.7682 (m-10) REVERT: R 24 TYR cc_start: 0.8041 (m-10) cc_final: 0.7783 (m-10) REVERT: S 18 SER cc_start: 0.9071 (t) cc_final: 0.8860 (m) REVERT: W 44 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8562 (ttpt) REVERT: CA 43 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8501 (mtmt) REVERT: HA 24 TYR cc_start: 0.7952 (m-10) cc_final: 0.7721 (m-10) REVERT: JA 40 LYS cc_start: 0.8667 (tttt) cc_final: 0.8455 (tttt) outliers start: 30 outliers final: 12 residues processed: 344 average time/residue: 0.2479 time to fit residues: 116.1488 Evaluate side-chains 306 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 293 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 5 ASP Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 5 ASP Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain DA residue 5 ASP 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: 2.9990 chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8303 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 11185 Z= 0.170 Angle : 0.376 4.526 15130 Z= 0.224 Chirality : 0.034 0.121 1785 Planarity : 0.002 0.018 1820 Dihedral : 6.861 82.429 1535 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 1.90 % Allowed : 16.38 % Favored : 81.72 % 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: 3.80 (0.11), residues: 1350 sheet: None (None), residues: 0 loop : 1.01 (0.30), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPFA 26 PHE 0.021 0.001 PHEAA 11 TYR 0.011 0.001 TYRFA 21 ARG 0.002 0.000 ARG J 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 327 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 306 time to evaluate : 1.397 Fit side-chains REVERT: G 44 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8666 (tttp) REVERT: T 40 LYS cc_start: 0.8726 (tttt) cc_final: 0.8476 (tttt) REVERT: BA 18 SER cc_start: 0.8890 (t) cc_final: 0.8659 (m) REVERT: JA 20 GLU cc_start: 0.6601 (tt0) cc_final: 0.6212 (tt0) outliers start: 21 outliers final: 17 residues processed: 314 average time/residue: 0.2388 time to fit residues: 103.0487 Evaluate side-chains 303 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 286 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain N residue 5 ASP Chi-restraints excluded: chain O residue 47 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain V residue 5 ASP Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain W residue 47 SER Chi-restraints excluded: chain AA residue 46 THR Chi-restraints excluded: chain CA residue 47 SER Chi-restraints excluded: chain DA residue 5 ASP Chi-restraints excluded: chain EA residue 47 SER Chi-restraints excluded: chain GA residue 31 SER 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: 7.9990 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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: 0.8375 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11185 Z= 0.238 Angle : 0.410 5.728 15130 Z= 0.242 Chirality : 0.035 0.116 1785 Planarity : 0.003 0.022 1820 Dihedral : 6.622 81.408 1535 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 3.80 % Allowed : 16.74 % Favored : 79.46 % 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: 5.66 (0.19), residues: 1385 helix: 3.72 (0.12), residues: 1350 sheet: None (None), residues: 0 loop : 0.58 (0.40), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPFA 26 PHE 0.023 0.001 PHEAA 11 TYR 0.015 0.001 TYRJA 24 ARG 0.001 0.000 ARGGA 18 *********************** 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 329 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 287 time to evaluate : 1.335 Fit side-chains REVERT: A 22 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8271 (tp) REVERT: N 22 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8539 (tp) REVERT: T 40 LYS cc_start: 0.8659 (tttt) cc_final: 0.8398 (tttt) REVERT: BA 18 SER cc_start: 0.8908 (t) cc_final: 0.8666 (m) REVERT: DA 22 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8227 (tp) REVERT: JA 20 GLU cc_start: 0.6628 (tt0) cc_final: 0.5992 (tt0) REVERT: JA 40 LYS cc_start: 0.8382 (tttt) cc_final: 0.8021 (tttt) outliers start: 42 outliers final: 32 residues processed: 310 average time/residue: 0.2471 time to fit residues: 105.0957 Evaluate side-chains 316 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 281 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 5 ASP 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 5 ASP Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 5 ASP Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain O 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 46 THR Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 5 ASP 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 W residue 47 SER Chi-restraints excluded: chain X residue 47 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 5 ASP 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 36 THR 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: 0.9980 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8323 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11185 Z= 0.175 Angle : 0.383 5.409 15130 Z= 0.227 Chirality : 0.034 0.127 1785 Planarity : 0.003 0.022 1820 Dihedral : 6.238 81.633 1535 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.71 % Allowed : 18.10 % Favored : 79.19 % 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: 5.92 (0.18), residues: 1385 helix: 3.84 (0.11), residues: 1375 sheet: None (None), residues: 0 loop : -1.69 (0.68), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Z 26 PHE 0.019 0.001 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 333 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 303 time to evaluate : 1.107 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.7882 (tp) REVERT: T 40 LYS cc_start: 0.8621 (tttt) cc_final: 0.8379 (tttt) REVERT: BA 18 SER cc_start: 0.8946 (t) cc_final: 0.8669 (m) REVERT: JA 40 LYS cc_start: 0.8419 (tttt) cc_final: 0.8050 (tttt) outliers start: 30 outliers final: 24 residues processed: 314 average time/residue: 0.2381 time to fit residues: 103.1128 Evaluate side-chains 315 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 290 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain N residue 5 ASP 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 47 SER Chi-restraints excluded: chain V residue 5 ASP Chi-restraints excluded: chain V residue 22 ILE 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 DA residue 5 ASP Chi-restraints excluded: chain DA residue 31 VAL Chi-restraints excluded: chain DA residue 44 LYS Chi-restraints excluded: chain EA residue 47 SER Chi-restraints excluded: chain GA residue 1 MET 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: 3.9990 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.8315 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11185 Z= 0.170 Angle : 0.384 5.878 15130 Z= 0.225 Chirality : 0.034 0.127 1785 Planarity : 0.003 0.021 1820 Dihedral : 6.035 79.911 1535 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 3.53 % Allowed : 19.19 % Favored : 77.29 % 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: 5.88 (0.18), residues: 1385 helix: 3.87 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.49 (0.49), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 26 PHE 0.024 0.001 PHE E 11 TYR 0.014 0.001 TYR T 24 ARG 0.000 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 341 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 302 time to evaluate : 1.206 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.7802 (tp) REVERT: Z 40 LYS cc_start: 0.8318 (ttpp) cc_final: 0.8082 (ttpp) REVERT: A 22 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8195 (tp) REVERT: N 22 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8459 (tp) REVERT: T 36 THR cc_start: 0.8985 (t) cc_final: 0.8755 (p) REVERT: T 40 LYS cc_start: 0.8576 (tttt) cc_final: 0.8353 (tttt) REVERT: BA 18 SER cc_start: 0.8902 (t) cc_final: 0.8654 (m) REVERT: DA 22 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8220 (tp) REVERT: JA 40 LYS cc_start: 0.8443 (tttt) cc_final: 0.8026 (tttt) outliers start: 39 outliers final: 31 residues processed: 324 average time/residue: 0.2411 time to fit residues: 110.0916 Evaluate side-chains 327 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 292 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain B residue 29 VAL 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 5 ASP Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 5 ASP Chi-restraints excluded: chain N residue 22 ILE Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain O residue 47 SER Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain V residue 5 ASP 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 DA residue 5 ASP 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 EA residue 47 SER 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: 5.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: HA 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11185 Z= 0.169 Angle : 0.390 7.198 15130 Z= 0.227 Chirality : 0.034 0.124 1785 Planarity : 0.003 0.021 1820 Dihedral : 5.866 78.847 1535 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 3.35 % Allowed : 20.00 % Favored : 76.65 % 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: 5.91 (0.18), residues: 1385 helix: 3.89 (0.11), residues: 1345 sheet: None (None), residues: 0 loop : 0.59 (0.49), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP W 26 PHE 0.030 0.001 PHE R 11 TYR 0.016 0.001 TYRAA 24 ARG 0.001 0.000 ARG S 33 *********************** 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 340 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 303 time to evaluate : 1.386 Fit side-chains REVERT: Z 22 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.7865 (tp) REVERT: Z 40 LYS cc_start: 0.8369 (ttpp) cc_final: 0.8156 (ttpp) REVERT: BA 18 SER cc_start: 0.8940 (t) cc_final: 0.8659 (m) REVERT: DA 22 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8220 (tp) REVERT: JA 40 LYS cc_start: 0.8414 (tttt) cc_final: 0.7981 (tttt) outliers start: 37 outliers final: 33 residues processed: 320 average time/residue: 0.2306 time to fit residues: 102.7244 Evaluate side-chains 329 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 294 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain B residue 29 VAL 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 5 ASP Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain I residue 47 SER Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 47 SER Chi-restraints excluded: chain N residue 5 ASP 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 V residue 5 ASP Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain W residue 47 SER Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain X residue 47 SER 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 5 ASP 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 EA residue 47 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.1547 > 50: distance: 43 - 60: 4.073 distance: 47 - 64: 12.349 distance: 51 - 69: 13.619 distance: 55 - 60: 3.061 distance: 56 - 76: 6.053 distance: 60 - 61: 7.001 distance: 61 - 62: 6.293 distance: 62 - 64: 6.345 distance: 63 - 84: 19.086 distance: 65 - 66: 3.330 distance: 65 - 68: 3.086 distance: 66 - 67: 3.404 distance: 66 - 69: 3.025 distance: 67 - 88: 9.058 distance: 69 - 70: 8.229 distance: 70 - 71: 6.633 distance: 70 - 73: 8.477 distance: 71 - 72: 3.161 distance: 71 - 76: 6.862 distance: 72 - 96: 15.813 distance: 73 - 74: 14.782 distance: 73 - 75: 16.100 distance: 76 - 77: 8.922 distance: 77 - 78: 16.460 distance: 77 - 80: 18.965 distance: 78 - 79: 7.712 distance: 78 - 84: 7.041 distance: 79 - 105: 12.603 distance: 80 - 81: 5.271 distance: 80 - 82: 16.734 distance: 81 - 83: 10.876 distance: 84 - 85: 4.724 distance: 85 - 86: 4.191 distance: 86 - 87: 5.044 distance: 86 - 88: 9.272 distance: 87 - 113: 17.701 distance: 88 - 89: 5.799 distance: 89 - 90: 3.977 distance: 89 - 92: 7.079 distance: 90 - 91: 6.263 distance: 92 - 93: 8.321 distance: 92 - 94: 7.092 distance: 93 - 95: 16.761 distance: 96 - 97: 5.163 distance: 97 - 98: 12.318 distance: 97 - 100: 6.797 distance: 98 - 99: 13.348 distance: 98 - 105: 16.819 distance: 99 - 133: 6.207 distance: 100 - 101: 5.140 distance: 101 - 102: 6.015 distance: 102 - 103: 6.372 distance: 103 - 104: 9.611 distance: 105 - 106: 24.566 distance: 106 - 107: 12.097 distance: 106 - 109: 25.613 distance: 107 - 108: 5.326 distance: 107 - 113: 5.899 distance: 108 - 140: 26.517 distance: 109 - 110: 38.689 distance: 110 - 111: 23.458 distance: 110 - 112: 31.772 distance: 113 - 114: 10.925 distance: 114 - 115: 5.664 distance: 114 - 117: 7.170 distance: 115 - 116: 4.304 distance: 116 - 147: 8.042 distance: 117 - 118: 12.832 distance: 118 - 119: 7.737 distance: 118 - 120: 10.537 distance: 119 - 121: 6.439 distance: 120 - 122: 4.774 distance: 121 - 123: 9.581 distance: 122 - 123: 7.335 distance: 124 - 125: 5.710 distance: 125 - 126: 3.619 distance: 125 - 128: 3.475 distance: 126 - 127: 4.130 distance: 127 - 153: 5.963 distance: 128 - 129: 13.441 distance: 129 - 130: 14.030 distance: 130 - 131: 16.250 distance: 131 - 132: 7.263