Starting phenix.real_space_refine on Thu Sep 26 14:37:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixj_35793/09_2024/8ixj_35793.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixj_35793/09_2024/8ixj_35793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixj_35793/09_2024/8ixj_35793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixj_35793/09_2024/8ixj_35793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixj_35793/09_2024/8ixj_35793.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixj_35793/09_2024/8ixj_35793.cif" } resolution = 3.1 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= 0.004 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 40 5.16 5 C 9080 2.51 5 N 2160 2.21 5 O 2480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13760 Number of models: 1 Model: "" Number of chains: 40 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: "L" 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: 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: "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: "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: 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: "D" 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: "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: "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: "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: 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: "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: 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: "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: 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: "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: "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: 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: "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: 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: "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: 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: "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} Chain: "KA" 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: "LA" 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: "MA" 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: "NA" 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: "OA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Time building chain proxies: 8.26, per 1000 atoms: 0.60 Number of scatterers: 13760 At special positions: 0 Unit cell: (78.57, 80.51, 194.97, 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 40 16.00 O 2480 8.00 N 2160 7.00 C 9080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 1.9 seconds 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 97.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'B' and resid 5 through 50 Processing helix chain 'C' and resid 6 through 50 Processing helix chain 'L' and resid 6 through 50 Processing helix chain 'F' and resid 6 through 50 Processing helix chain 'G' and resid 6 through 50 Processing helix chain 'H' and resid 6 through 50 Processing helix chain 'I' and resid 6 through 50 Processing helix chain 'J' and resid 6 through 50 removed outlier: 3.940A pdb=" N VAL J 30 " --> pdb=" O TRP J 26 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL J 31 " --> pdb=" O ALA J 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 50 Processing helix chain 'D' and resid 6 through 50 Processing helix chain 'E' and resid 6 through 50 Processing helix chain 'K' and resid 6 through 50 Processing helix chain 'M' and resid 6 through 50 Processing helix chain 'N' and resid 6 through 50 Processing helix chain 'O' and resid 6 through 50 Processing helix chain 'P' and resid 6 through 50 removed outlier: 3.940A pdb=" N VAL P 30 " --> pdb=" O TRP P 26 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL P 31 " --> pdb=" O ALA P 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 50 Processing helix chain 'R' and resid 6 through 50 Processing helix chain 'S' and resid 6 through 50 Processing helix chain 'T' and resid 6 through 50 Processing helix chain 'V' and resid 6 through 50 Processing helix chain 'W' and resid 6 through 50 Processing helix chain 'X' and resid 6 through 50 Processing helix chain 'Y' and resid 6 through 50 removed outlier: 3.940A pdb=" N VAL Y 30 " --> pdb=" O TRP Y 26 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL Y 31 " --> pdb=" O ALA Y 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 6 through 50 Processing helix chain 'AA' and resid 6 through 50 Processing helix chain 'BA' and resid 6 through 50 Processing helix chain 'CA' and resid 6 through 50 Processing helix chain 'DA' and resid 6 through 50 Processing helix chain 'EA' and resid 6 through 50 Processing helix chain 'FA' and resid 6 through 50 Processing helix chain 'GA' and resid 6 through 50 removed outlier: 3.940A pdb=" N VALGA 30 " --> pdb=" O TRPGA 26 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VALGA 31 " --> pdb=" O ALAGA 27 " (cutoff:3.500A) Processing helix chain 'HA' and resid 6 through 50 Processing helix chain 'IA' and resid 6 through 50 Processing helix chain 'JA' and resid 6 through 50 Processing helix chain 'KA' and resid 6 through 50 Processing helix chain 'LA' and resid 6 through 50 Processing helix chain 'MA' and resid 6 through 50 Processing helix chain 'NA' and resid 6 through 50 Processing helix chain 'OA' and resid 6 through 50 removed outlier: 3.940A pdb=" N VALOA 30 " --> pdb=" O TRPOA 26 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VALOA 31 " --> pdb=" O ALAOA 27 " (cutoff:3.500A) 1631 hydrogen bonds defined for protein. 4893 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: 4.14 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2507 1.34 - 1.45: 3463 1.45 - 1.57: 7990 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 14040 Sorted by residual: bond pdb=" N VALIA 31 " pdb=" CA VALIA 31 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.96e+00 bond pdb=" N VALGA 29 " pdb=" CA VALGA 29 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.88e+00 bond pdb=" N VAL Y 29 " pdb=" CA VAL Y 29 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.87e+00 bond pdb=" N VAL C 31 " pdb=" CA VAL C 31 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.77e+00 bond pdb=" N VALOA 29 " pdb=" CA VALOA 29 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.72e+00 ... (remaining 14035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 11431 1.14 - 2.28: 4401 2.28 - 3.43: 3084 3.43 - 4.57: 34 4.57 - 5.71: 50 Bond angle restraints: 19000 Sorted by residual: angle pdb=" N PROMA 6 " pdb=" CA PROMA 6 " pdb=" C PROMA 6 " ideal model delta sigma weight residual 113.84 108.13 5.71 1.30e+00 5.92e-01 1.93e+01 angle pdb=" N PRO W 6 " pdb=" CA PRO W 6 " pdb=" C PRO W 6 " ideal model delta sigma weight residual 113.84 108.14 5.70 1.30e+00 5.92e-01 1.92e+01 angle pdb=" N PRO N 6 " pdb=" CA PRO N 6 " pdb=" C PRO N 6 " ideal model delta sigma weight residual 113.84 108.15 5.69 1.30e+00 5.92e-01 1.92e+01 angle pdb=" N PRO H 6 " pdb=" CA PRO H 6 " pdb=" C PRO H 6 " ideal model delta sigma weight residual 113.84 108.15 5.69 1.30e+00 5.92e-01 1.92e+01 angle pdb=" N PROEA 6 " pdb=" CA PROEA 6 " pdb=" C PROEA 6 " ideal model delta sigma weight residual 113.65 108.11 5.54 1.35e+00 5.49e-01 1.68e+01 ... (remaining 18995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.95: 7130 9.95 - 19.91: 702 19.91 - 29.86: 228 29.86 - 39.81: 115 39.81 - 49.77: 25 Dihedral angle restraints: 8200 sinusoidal: 2880 harmonic: 5320 Sorted by residual: dihedral pdb=" N LEUMA 14 " pdb=" CA LEUMA 14 " pdb=" CB LEUMA 14 " pdb=" CG LEUMA 14 " ideal model delta sinusoidal sigma weight residual -60.00 -109.77 49.77 3 1.50e+01 4.44e-03 8.82e+00 dihedral pdb=" N LEU W 14 " pdb=" CA LEU W 14 " pdb=" CB LEU W 14 " pdb=" CG LEU W 14 " ideal model delta sinusoidal sigma weight residual -60.00 -109.75 49.75 3 1.50e+01 4.44e-03 8.81e+00 dihedral pdb=" N LEU N 14 " pdb=" CA LEU N 14 " pdb=" CB LEU N 14 " pdb=" CG LEU N 14 " ideal model delta sinusoidal sigma weight residual -60.00 -109.75 49.75 3 1.50e+01 4.44e-03 8.81e+00 ... (remaining 8197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 530 0.040 - 0.080: 632 0.080 - 0.120: 661 0.120 - 0.160: 310 0.160 - 0.200: 107 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CB VALIA 31 " pdb=" CA VALIA 31 " pdb=" CG1 VALIA 31 " pdb=" CG2 VALIA 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CB VALAA 31 " pdb=" CA VALAA 31 " pdb=" CG1 VALAA 31 " pdb=" CG2 VALAA 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CB VAL D 31 " pdb=" CA VAL D 31 " pdb=" CG1 VAL D 31 " pdb=" CG2 VAL D 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.58e-01 ... (remaining 2237 not shown) Planarity restraints: 2280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO Y 6 " 0.010 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C PRO Y 6 " -0.038 2.00e-02 2.50e+03 pdb=" O PRO Y 6 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA Y 7 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PROOA 6 " -0.010 2.00e-02 2.50e+03 2.21e-02 4.86e+00 pdb=" C PROOA 6 " 0.038 2.00e-02 2.50e+03 pdb=" O PROOA 6 " -0.015 2.00e-02 2.50e+03 pdb=" N ALAOA 7 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO J 6 " -0.010 2.00e-02 2.50e+03 2.20e-02 4.82e+00 pdb=" C PRO J 6 " 0.038 2.00e-02 2.50e+03 pdb=" O PRO J 6 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA J 7 " -0.013 2.00e-02 2.50e+03 ... (remaining 2277 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 5230 2.91 - 3.41: 15533 3.41 - 3.90: 23177 3.90 - 4.40: 24320 4.40 - 4.90: 42826 Nonbonded interactions: 111086 Sorted by model distance: nonbonded pdb=" O PHEHA 42 " pdb=" OG1 THRHA 46 " model vdw 2.412 3.040 nonbonded pdb=" O PHE B 42 " pdb=" OG1 THR B 46 " model vdw 2.412 3.040 nonbonded pdb=" O PHE Z 42 " pdb=" OG1 THR Z 46 " model vdw 2.412 3.040 nonbonded pdb=" O PHE Q 42 " pdb=" OG1 THR Q 46 " model vdw 2.412 3.040 nonbonded pdb=" O PHE A 42 " pdb=" OG1 THR A 46 " model vdw 2.413 3.040 ... (remaining 111081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'AA' selection = chain 'B' selection = chain 'BA' selection = chain 'C' selection = chain 'CA' selection = chain 'D' selection = chain 'DA' selection = chain 'E' selection = chain 'EA' selection = chain 'F' selection = chain 'FA' selection = chain 'G' selection = chain 'GA' selection = chain 'H' selection = chain 'HA' selection = chain 'I' selection = chain 'IA' selection = chain 'J' selection = chain 'JA' selection = chain 'K' selection = chain 'KA' selection = chain 'L' selection = chain 'LA' selection = chain 'M' selection = chain 'MA' selection = chain 'N' selection = chain 'NA' selection = chain 'O' selection = chain 'OA' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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 individual isotropic 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: 0.700 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 31.740 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 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 0.038 14040 Z= 0.768 Angle : 1.449 5.711 19000 Z= 1.229 Chirality : 0.092 0.200 2240 Planarity : 0.004 0.022 2280 Dihedral : 10.466 49.766 4760 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.16), residues: 1760 helix: 2.29 (0.10), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 26 PHE 0.012 0.002 PHEOA 11 TYR 0.012 0.002 TYR P 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.568 Fit side-chains REVERT: B 12 ASN cc_start: 0.8139 (m-40) cc_final: 0.7673 (m110) REVERT: L 44 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8445 (ttpp) REVERT: F 12 ASN cc_start: 0.8178 (m-40) cc_final: 0.7970 (m-40) REVERT: F 44 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7855 (tttt) REVERT: A 12 ASN cc_start: 0.8199 (m-40) cc_final: 0.7865 (m110) REVERT: D 21 TYR cc_start: 0.8374 (m-10) cc_final: 0.8090 (m-10) REVERT: D 47 SER cc_start: 0.8689 (t) cc_final: 0.8477 (m) REVERT: K 12 ASN cc_start: 0.8220 (m-40) cc_final: 0.8013 (m110) REVERT: Q 12 ASN cc_start: 0.8130 (m-40) cc_final: 0.7828 (m110) REVERT: R 21 TYR cc_start: 0.8203 (m-10) cc_final: 0.7632 (m-80) REVERT: R 47 SER cc_start: 0.8685 (t) cc_final: 0.8358 (m) REVERT: S 44 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8510 (ttpp) REVERT: AA 21 TYR cc_start: 0.8189 (m-10) cc_final: 0.7852 (m-10) REVERT: AA 47 SER cc_start: 0.8595 (t) cc_final: 0.8237 (m) REVERT: CA 12 ASN cc_start: 0.8279 (m-40) cc_final: 0.8073 (m110) REVERT: HA 12 ASN cc_start: 0.8306 (m-40) cc_final: 0.8102 (m-40) REVERT: IA 21 TYR cc_start: 0.8190 (m-10) cc_final: 0.7805 (m-10) REVERT: OA 40 LYS cc_start: 0.8477 (tttt) cc_final: 0.8190 (ttpt) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.3370 time to fit residues: 95.6408 Evaluate side-chains 171 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 125 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 ASN H 12 ASN M 12 ASN N 12 ASN T 12 ASN V 12 ASN W 12 ASN DA 12 ASN EA 12 ASN KA 12 ASN LA 12 ASN MA 12 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 14040 Z= 0.142 Angle : 0.332 3.582 19000 Z= 0.200 Chirality : 0.031 0.107 2240 Planarity : 0.002 0.012 2280 Dihedral : 3.906 49.711 1920 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.29 % Allowed : 6.32 % Favored : 93.38 % 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: 6.76 (0.14), residues: 1760 helix: 4.32 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRPBA 26 PHE 0.008 0.001 PHE E 11 TYR 0.011 0.001 TYRKA 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 260 time to evaluate : 1.538 Fit side-chains REVERT: C 21 TYR cc_start: 0.8271 (m-10) cc_final: 0.7994 (m-80) REVERT: F 44 LYS cc_start: 0.8096 (ttmm) cc_final: 0.7858 (tttt) REVERT: F 46 THR cc_start: 0.8549 (m) cc_final: 0.8313 (p) REVERT: G 46 THR cc_start: 0.8238 (m) cc_final: 0.7920 (p) REVERT: M 46 THR cc_start: 0.8258 (m) cc_final: 0.7932 (p) REVERT: P 40 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8393 (ttpt) REVERT: V 42 PHE cc_start: 0.8606 (t80) cc_final: 0.8256 (t80) REVERT: V 43 LYS cc_start: 0.8383 (ttmm) cc_final: 0.8133 (mtpt) REVERT: V 46 THR cc_start: 0.8293 (m) cc_final: 0.8047 (p) REVERT: AA 21 TYR cc_start: 0.8209 (m-10) cc_final: 0.7926 (m-80) REVERT: BA 44 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8503 (ttpp) REVERT: CA 40 LYS cc_start: 0.8482 (tttt) cc_final: 0.8269 (tttt) REVERT: DA 46 THR cc_start: 0.8233 (m) cc_final: 0.7954 (p) REVERT: GA 40 LYS cc_start: 0.8816 (ttmm) cc_final: 0.8533 (ttpp) REVERT: IA 21 TYR cc_start: 0.8319 (m-10) cc_final: 0.8058 (m-80) REVERT: LA 46 THR cc_start: 0.8183 (m) cc_final: 0.7878 (p) outliers start: 4 outliers final: 2 residues processed: 262 average time/residue: 0.3158 time to fit residues: 112.2372 Evaluate side-chains 217 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 215 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 13 SER Chi-restraints excluded: chain HA residue 28 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 0.0070 chunk 98 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 12 ASN N 12 ASN W 12 ASN EA 12 ASN MA 12 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14040 Z= 0.175 Angle : 0.331 3.546 19000 Z= 0.197 Chirality : 0.031 0.090 2240 Planarity : 0.002 0.015 2280 Dihedral : 3.301 39.909 1920 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.74 % Allowed : 9.85 % Favored : 89.41 % 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: 7.09 (0.14), residues: 1760 helix: 4.52 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 26 PHE 0.006 0.001 PHE B 45 TYR 0.013 0.002 TYR D 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 264 time to evaluate : 1.592 Fit side-chains REVERT: C 21 TYR cc_start: 0.8334 (m-10) cc_final: 0.8060 (m-80) REVERT: L 44 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8571 (ttpp) REVERT: F 44 LYS cc_start: 0.8240 (ttmm) cc_final: 0.8005 (tttt) REVERT: G 42 PHE cc_start: 0.8614 (t80) cc_final: 0.8351 (t80) REVERT: G 43 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8177 (mtpt) REVERT: G 46 THR cc_start: 0.8307 (m) cc_final: 0.7924 (p) REVERT: M 46 THR cc_start: 0.8162 (m) cc_final: 0.7790 (p) REVERT: O 48 LYS cc_start: 0.8510 (mptt) cc_final: 0.8290 (mptt) REVERT: Q 12 ASN cc_start: 0.8275 (m-40) cc_final: 0.7794 (m110) REVERT: V 42 PHE cc_start: 0.8571 (t80) cc_final: 0.8327 (t80) REVERT: V 43 LYS cc_start: 0.8480 (ttmm) cc_final: 0.8153 (mtpt) REVERT: V 46 THR cc_start: 0.8277 (m) cc_final: 0.7966 (p) REVERT: Y 40 LYS cc_start: 0.9169 (ttpp) cc_final: 0.8864 (ttpp) REVERT: AA 21 TYR cc_start: 0.8344 (m-10) cc_final: 0.8034 (m-80) REVERT: BA 44 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8589 (ttpp) REVERT: DA 43 LYS cc_start: 0.8471 (ttmm) cc_final: 0.8133 (mtpt) REVERT: DA 46 THR cc_start: 0.8143 (m) cc_final: 0.7783 (p) REVERT: GA 40 LYS cc_start: 0.8967 (ttmm) cc_final: 0.8633 (ttpp) REVERT: IA 21 TYR cc_start: 0.8371 (m-10) cc_final: 0.8093 (m-80) REVERT: JA 44 LYS cc_start: 0.8883 (ttmm) cc_final: 0.8646 (ttpp) REVERT: LA 8 LYS cc_start: 0.7707 (tttp) cc_final: 0.7422 (ttmm) REVERT: LA 46 THR cc_start: 0.8180 (m) cc_final: 0.7827 (p) outliers start: 10 outliers final: 7 residues processed: 265 average time/residue: 0.3138 time to fit residues: 113.9288 Evaluate side-chains 252 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 245 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain AA residue 47 SER Chi-restraints excluded: chain GA residue 47 SER Chi-restraints excluded: chain OA residue 47 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 138 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 12 ASN N 12 ASN W 12 ASN DA 12 ASN EA 12 ASN MA 12 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14040 Z= 0.170 Angle : 0.318 3.470 19000 Z= 0.191 Chirality : 0.031 0.179 2240 Planarity : 0.002 0.018 2280 Dihedral : 3.204 47.614 1920 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.66 % Allowed : 11.25 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 7.01 (0.14), residues: 1760 helix: 4.47 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 26 PHE 0.007 0.001 PHE E 45 TYR 0.016 0.001 TYRHA 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 256 time to evaluate : 1.373 Fit side-chains REVERT: C 21 TYR cc_start: 0.8394 (m-10) cc_final: 0.8093 (m-80) REVERT: F 44 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7956 (tttt) REVERT: G 46 THR cc_start: 0.8329 (m) cc_final: 0.7941 (p) REVERT: M 46 THR cc_start: 0.8107 (m) cc_final: 0.7741 (p) REVERT: O 48 LYS cc_start: 0.8497 (mptt) cc_final: 0.8282 (mptt) REVERT: Q 12 ASN cc_start: 0.8276 (m-40) cc_final: 0.7916 (m110) REVERT: S 48 LYS cc_start: 0.8522 (mmtm) cc_final: 0.7905 (mmmt) REVERT: T 28 MET cc_start: 0.8876 (ttp) cc_final: 0.8572 (ttt) REVERT: V 43 LYS cc_start: 0.8455 (ttmm) cc_final: 0.8093 (mtpt) REVERT: V 46 THR cc_start: 0.8237 (m) cc_final: 0.7882 (p) REVERT: Y 40 LYS cc_start: 0.9137 (ttpp) cc_final: 0.8887 (ttpp) REVERT: AA 21 TYR cc_start: 0.8400 (m-10) cc_final: 0.8057 (m-80) REVERT: BA 44 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8593 (ttpp) REVERT: DA 43 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8141 (mtpt) REVERT: DA 46 THR cc_start: 0.8160 (m) cc_final: 0.7786 (p) REVERT: GA 40 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8620 (ttpp) REVERT: IA 21 TYR cc_start: 0.8438 (m-10) cc_final: 0.8088 (m-80) REVERT: JA 44 LYS cc_start: 0.8887 (ttmm) cc_final: 0.8672 (ttpp) REVERT: JA 48 LYS cc_start: 0.8465 (mttm) cc_final: 0.7979 (mtpt) REVERT: KA 28 MET cc_start: 0.8654 (ttp) cc_final: 0.8425 (ttt) REVERT: LA 8 LYS cc_start: 0.7736 (tttp) cc_final: 0.7429 (ttmm) REVERT: LA 46 THR cc_start: 0.8184 (m) cc_final: 0.7815 (p) REVERT: MA 29 VAL cc_start: 0.9296 (t) cc_final: 0.9081 (p) REVERT: OA 20 GLU cc_start: 0.7907 (tt0) cc_final: 0.7610 (tt0) outliers start: 9 outliers final: 6 residues processed: 258 average time/residue: 0.3041 time to fit residues: 107.0240 Evaluate side-chains 252 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 246 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain N residue 48 LYS Chi-restraints excluded: chain EA residue 48 LYS Chi-restraints excluded: chain KA residue 44 LYS Chi-restraints excluded: chain OA residue 47 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 14040 Z= 0.169 Angle : 0.313 3.762 19000 Z= 0.188 Chirality : 0.030 0.096 2240 Planarity : 0.002 0.020 2280 Dihedral : 3.118 44.842 1920 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.66 % Allowed : 12.21 % Favored : 87.13 % 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: 7.00 (0.14), residues: 1760 helix: 4.47 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 26 PHE 0.007 0.001 PHE E 45 TYR 0.020 0.001 TYRHA 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 255 time to evaluate : 1.703 Fit side-chains REVERT: C 21 TYR cc_start: 0.8404 (m-10) cc_final: 0.8096 (m-80) REVERT: F 44 LYS cc_start: 0.8226 (ttmm) cc_final: 0.7981 (tttt) REVERT: G 46 THR cc_start: 0.8354 (m) cc_final: 0.7933 (p) REVERT: M 46 THR cc_start: 0.8124 (m) cc_final: 0.7752 (p) REVERT: S 48 LYS cc_start: 0.8519 (mmtm) cc_final: 0.7877 (mmmt) REVERT: T 28 MET cc_start: 0.8829 (ttp) cc_final: 0.8551 (ttt) REVERT: V 43 LYS cc_start: 0.8424 (ttmm) cc_final: 0.8097 (mtpt) REVERT: V 46 THR cc_start: 0.8254 (m) cc_final: 0.7904 (p) REVERT: Y 40 LYS cc_start: 0.9149 (ttpp) cc_final: 0.8908 (ttpp) REVERT: AA 21 TYR cc_start: 0.8406 (m-10) cc_final: 0.8015 (m-80) REVERT: BA 44 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8584 (ttpp) REVERT: DA 43 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8076 (mtpt) REVERT: DA 46 THR cc_start: 0.8207 (m) cc_final: 0.7821 (p) REVERT: JA 44 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8685 (ttpp) REVERT: LA 8 LYS cc_start: 0.7726 (tttp) cc_final: 0.7425 (ttmm) REVERT: LA 46 THR cc_start: 0.8193 (m) cc_final: 0.7781 (p) REVERT: OA 40 LYS cc_start: 0.9234 (ttpp) cc_final: 0.8990 (ttpt) outliers start: 9 outliers final: 7 residues processed: 256 average time/residue: 0.3099 time to fit residues: 109.9641 Evaluate side-chains 256 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 249 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain N residue 48 LYS Chi-restraints excluded: chain W residue 48 LYS Chi-restraints excluded: chain EA residue 48 LYS Chi-restraints excluded: chain GA residue 47 SER Chi-restraints excluded: chain KA residue 44 LYS Chi-restraints excluded: chain OA residue 36 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.8394 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14040 Z= 0.151 Angle : 0.303 3.475 19000 Z= 0.183 Chirality : 0.030 0.092 2240 Planarity : 0.002 0.017 2280 Dihedral : 3.025 47.464 1920 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.74 % Allowed : 12.50 % Favored : 86.76 % 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: 7.14 (0.14), residues: 1760 helix: 4.56 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRPDA 26 PHE 0.006 0.001 PHE E 45 TYR 0.020 0.001 TYRHA 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 251 time to evaluate : 1.431 Fit side-chains REVERT: F 44 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7960 (tttt) REVERT: G 46 THR cc_start: 0.8341 (m) cc_final: 0.7939 (p) REVERT: M 46 THR cc_start: 0.8114 (m) cc_final: 0.7727 (p) REVERT: S 48 LYS cc_start: 0.8497 (mmtm) cc_final: 0.7866 (mmmt) REVERT: T 28 MET cc_start: 0.8814 (ttp) cc_final: 0.8545 (ttt) REVERT: V 43 LYS cc_start: 0.8383 (ttmm) cc_final: 0.8022 (mtpt) REVERT: V 46 THR cc_start: 0.8272 (m) cc_final: 0.7931 (p) REVERT: Y 40 LYS cc_start: 0.9143 (ttpp) cc_final: 0.8910 (ttpp) REVERT: AA 21 TYR cc_start: 0.8408 (m-10) cc_final: 0.7998 (m-80) REVERT: BA 44 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8587 (ttpp) REVERT: DA 43 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8119 (mtpt) REVERT: DA 46 THR cc_start: 0.8185 (m) cc_final: 0.7759 (p) REVERT: JA 44 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8696 (ttpp) REVERT: JA 48 LYS cc_start: 0.8463 (mttp) cc_final: 0.7973 (mtpt) REVERT: LA 8 LYS cc_start: 0.7670 (tttp) cc_final: 0.7386 (ttmm) REVERT: LA 46 THR cc_start: 0.8033 (m) cc_final: 0.7623 (p) outliers start: 10 outliers final: 8 residues processed: 251 average time/residue: 0.3142 time to fit residues: 108.3883 Evaluate side-chains 255 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 247 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain N residue 48 LYS Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain W residue 48 LYS Chi-restraints excluded: chain EA residue 48 LYS Chi-restraints excluded: chain GA residue 47 SER Chi-restraints excluded: chain OA residue 36 THR Chi-restraints excluded: chain OA residue 47 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 154 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 14040 Z= 0.130 Angle : 0.292 3.438 19000 Z= 0.177 Chirality : 0.030 0.095 2240 Planarity : 0.002 0.015 2280 Dihedral : 2.851 46.323 1920 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.66 % Allowed : 12.72 % Favored : 86.62 % 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: 7.31 (0.14), residues: 1760 helix: 4.66 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRPDA 26 PHE 0.007 0.001 PHE D 11 TYR 0.021 0.001 TYRHA 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 254 time to evaluate : 1.654 Fit side-chains REVERT: F 44 LYS cc_start: 0.8190 (ttmm) cc_final: 0.7961 (tttt) REVERT: G 46 THR cc_start: 0.8334 (m) cc_final: 0.7917 (p) REVERT: S 48 LYS cc_start: 0.8482 (mmtm) cc_final: 0.7880 (mmmt) REVERT: T 28 MET cc_start: 0.8785 (ttp) cc_final: 0.8527 (ttt) REVERT: V 43 LYS cc_start: 0.8356 (ttmm) cc_final: 0.7974 (mtpt) REVERT: V 46 THR cc_start: 0.8316 (m) cc_final: 0.7972 (p) REVERT: AA 21 TYR cc_start: 0.8403 (m-10) cc_final: 0.7990 (m-80) REVERT: BA 44 LYS cc_start: 0.8883 (ttmm) cc_final: 0.8553 (ttpp) REVERT: DA 43 LYS cc_start: 0.8359 (ttmm) cc_final: 0.8026 (mtpt) REVERT: DA 46 THR cc_start: 0.8178 (m) cc_final: 0.7751 (p) REVERT: LA 46 THR cc_start: 0.7921 (m) cc_final: 0.7455 (p) outliers start: 9 outliers final: 8 residues processed: 255 average time/residue: 0.3145 time to fit residues: 109.2568 Evaluate side-chains 250 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 242 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain W residue 48 LYS Chi-restraints excluded: chain Z residue 28 MET Chi-restraints excluded: chain EA residue 48 LYS Chi-restraints excluded: chain GA residue 47 SER Chi-restraints excluded: chain OA residue 36 THR Chi-restraints excluded: chain OA residue 47 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 12 ASN Q 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14040 Z= 0.151 Angle : 0.304 3.479 19000 Z= 0.184 Chirality : 0.031 0.111 2240 Planarity : 0.002 0.016 2280 Dihedral : 2.839 40.506 1920 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.96 % Allowed : 13.01 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 7.21 (0.14), residues: 1760 helix: 4.60 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRPDA 26 PHE 0.006 0.001 PHE E 45 TYR 0.022 0.001 TYRHA 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 250 time to evaluate : 1.576 Fit side-chains REVERT: C 21 TYR cc_start: 0.8455 (m-10) cc_final: 0.8163 (m-80) REVERT: F 12 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8339 (m110) REVERT: F 44 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7975 (tttt) REVERT: G 46 THR cc_start: 0.8317 (m) cc_final: 0.7913 (p) REVERT: S 48 LYS cc_start: 0.8520 (mmtm) cc_final: 0.7895 (mmmt) REVERT: T 28 MET cc_start: 0.8809 (ttp) cc_final: 0.8559 (ttt) REVERT: V 43 LYS cc_start: 0.8356 (ttmm) cc_final: 0.7972 (mtpt) REVERT: V 46 THR cc_start: 0.8313 (m) cc_final: 0.7978 (p) REVERT: AA 21 TYR cc_start: 0.8419 (m-10) cc_final: 0.7994 (m-80) REVERT: BA 44 LYS cc_start: 0.8900 (ttmm) cc_final: 0.8567 (ttpp) REVERT: DA 43 LYS cc_start: 0.8355 (ttmm) cc_final: 0.8023 (mtpt) REVERT: DA 46 THR cc_start: 0.8179 (m) cc_final: 0.7752 (p) REVERT: LA 46 THR cc_start: 0.7971 (m) cc_final: 0.7515 (p) outliers start: 13 outliers final: 11 residues processed: 251 average time/residue: 0.3028 time to fit residues: 104.6685 Evaluate side-chains 254 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 242 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain N residue 48 LYS Chi-restraints excluded: chain W residue 48 LYS Chi-restraints excluded: chain Z residue 28 MET Chi-restraints excluded: chain EA residue 48 LYS Chi-restraints excluded: chain GA residue 47 SER Chi-restraints excluded: chain HA residue 28 MET Chi-restraints excluded: chain KA residue 44 LYS Chi-restraints excluded: chain OA residue 36 THR Chi-restraints excluded: chain OA residue 47 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 86 optimal weight: 0.0770 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 14040 Z= 0.136 Angle : 0.298 3.458 19000 Z= 0.181 Chirality : 0.031 0.107 2240 Planarity : 0.002 0.024 2280 Dihedral : 2.801 41.323 1920 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.96 % Allowed : 12.94 % Favored : 86.10 % 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: 7.29 (0.14), residues: 1760 helix: 4.65 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRPDA 26 PHE 0.005 0.001 PHE B 45 TYR 0.022 0.001 TYRHA 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 242 time to evaluate : 1.592 Fit side-chains REVERT: C 21 TYR cc_start: 0.8455 (m-10) cc_final: 0.8153 (m-80) REVERT: F 44 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7965 (tttt) REVERT: G 46 THR cc_start: 0.8250 (m) cc_final: 0.7824 (p) REVERT: S 48 LYS cc_start: 0.8499 (mmtm) cc_final: 0.7885 (mmmt) REVERT: T 28 MET cc_start: 0.8788 (ttp) cc_final: 0.8549 (ttt) REVERT: V 43 LYS cc_start: 0.8328 (ttmm) cc_final: 0.8020 (mtpt) REVERT: V 46 THR cc_start: 0.8310 (m) cc_final: 0.7985 (p) REVERT: AA 21 TYR cc_start: 0.8411 (m-10) cc_final: 0.7982 (m-80) REVERT: BA 44 LYS cc_start: 0.8887 (ttmm) cc_final: 0.8629 (ttpp) REVERT: CA 40 LYS cc_start: 0.8547 (tttt) cc_final: 0.8315 (tttt) REVERT: DA 43 LYS cc_start: 0.8421 (ttmm) cc_final: 0.7974 (mtpt) REVERT: DA 46 THR cc_start: 0.8190 (m) cc_final: 0.7762 (p) REVERT: LA 46 THR cc_start: 0.8016 (m) cc_final: 0.7588 (p) outliers start: 13 outliers final: 11 residues processed: 243 average time/residue: 0.3133 time to fit residues: 104.2603 Evaluate side-chains 252 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 241 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain W residue 48 LYS Chi-restraints excluded: chain Z residue 28 MET Chi-restraints excluded: chain EA residue 48 LYS Chi-restraints excluded: chain GA residue 47 SER Chi-restraints excluded: chain HA residue 28 MET Chi-restraints excluded: chain KA residue 44 LYS Chi-restraints excluded: chain MA residue 48 LYS Chi-restraints excluded: chain OA residue 36 THR Chi-restraints excluded: chain OA residue 47 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 2.9990 chunk 92 optimal weight: 0.0970 chunk 72 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14040 Z= 0.139 Angle : 0.300 3.445 19000 Z= 0.183 Chirality : 0.031 0.108 2240 Planarity : 0.002 0.022 2280 Dihedral : 2.777 38.944 1920 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.88 % Allowed : 13.24 % Favored : 85.88 % 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: 7.25 (0.14), residues: 1760 helix: 4.62 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRPDA 26 PHE 0.005 0.001 PHE E 45 TYR 0.023 0.001 TYRHA 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 244 time to evaluate : 1.503 Fit side-chains REVERT: F 44 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7978 (tttt) REVERT: G 46 THR cc_start: 0.8259 (m) cc_final: 0.7829 (p) REVERT: S 48 LYS cc_start: 0.8493 (mmtm) cc_final: 0.7883 (mmmt) REVERT: T 28 MET cc_start: 0.8789 (ttp) cc_final: 0.8552 (ttt) REVERT: V 43 LYS cc_start: 0.8367 (ttmm) cc_final: 0.8066 (mtpt) REVERT: V 46 THR cc_start: 0.8298 (m) cc_final: 0.7973 (p) REVERT: BA 44 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8552 (ttpp) REVERT: CA 40 LYS cc_start: 0.8553 (tttt) cc_final: 0.8319 (tttt) REVERT: DA 43 LYS cc_start: 0.8419 (ttmm) cc_final: 0.7992 (mtpt) REVERT: DA 46 THR cc_start: 0.8206 (m) cc_final: 0.7797 (p) REVERT: LA 46 THR cc_start: 0.7983 (m) cc_final: 0.7518 (p) outliers start: 12 outliers final: 12 residues processed: 245 average time/residue: 0.2938 time to fit residues: 98.8892 Evaluate side-chains 253 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 241 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain W residue 48 LYS Chi-restraints excluded: chain Z residue 28 MET Chi-restraints excluded: chain EA residue 48 LYS Chi-restraints excluded: chain GA residue 47 SER Chi-restraints excluded: chain HA residue 28 MET Chi-restraints excluded: chain KA residue 44 LYS Chi-restraints excluded: chain MA residue 48 LYS Chi-restraints excluded: chain OA residue 36 THR Chi-restraints excluded: chain OA residue 47 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.119746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.090969 restraints weight = 16199.368| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.56 r_work: 0.3071 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14040 Z= 0.149 Angle : 0.308 4.055 19000 Z= 0.188 Chirality : 0.031 0.118 2240 Planarity : 0.002 0.021 2280 Dihedral : 2.825 36.929 1920 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.88 % Allowed : 13.09 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 7.19 (0.14), residues: 1760 helix: 4.58 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 26 PHE 0.006 0.001 PHE E 45 TYR 0.029 0.001 TYRHA 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2847.15 seconds wall clock time: 51 minutes 50.65 seconds (3110.65 seconds total)