Starting phenix.real_space_refine on Thu May 15 16:25:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ixj_35793/05_2025/8ixj_35793.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ixj_35793/05_2025/8ixj_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/cci-nas-00/data/ceres_data/8ixj_35793/05_2025/8ixj_35793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ixj_35793/05_2025/8ixj_35793.map" model { file = "/net/cci-nas-00/data/ceres_data/8ixj_35793/05_2025/8ixj_35793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ixj_35793/05_2025/8ixj_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-5687/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: 7.87, per 1000 atoms: 0.57 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: 3.18 Conformation dependent library (CDL) restraints added in 1.7 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: 0.84 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: 4.41 Time building geometry restraints manager: 3.73 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: 0.710 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: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 30.490 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.100 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.520 ------------------------------------------------------------------------------- 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= 0.929 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 Details of bonding type rmsd hydrogen bonds : bond 0.14374 ( 1631) hydrogen bonds : angle 4.61627 ( 4893) covalent geometry : bond 0.01208 (14040) covalent geometry : angle 1.44890 (19000) *********************** 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 to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.383 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: 0.3471 time to fit residues: 97.8802 Evaluate side-chains 171 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.121528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.093343 restraints weight = 16016.054| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.52 r_work: 0.3131 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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= 0.134 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 Details of bonding type rmsd hydrogen bonds : bond 0.05600 ( 1631) hydrogen bonds : angle 3.45959 ( 4893) covalent geometry : bond 0.00223 (14040) covalent geometry : angle 0.33229 (19000) *********************** 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 to be fit. rotamer outliers: 4 poor density : 260 time to evaluate : 1.365 Fit side-chains REVERT: C 21 TYR cc_start: 0.8275 (m-10) cc_final: 0.8058 (m-80) REVERT: F 44 LYS cc_start: 0.8105 (ttmm) cc_final: 0.7864 (tttt) REVERT: F 46 THR cc_start: 0.8612 (m) cc_final: 0.8367 (p) REVERT: G 46 THR cc_start: 0.8288 (m) cc_final: 0.7951 (p) REVERT: M 46 THR cc_start: 0.8295 (m) cc_final: 0.7950 (p) REVERT: P 40 LYS cc_start: 0.8801 (ttmm) cc_final: 0.8309 (ttpt) REVERT: V 42 PHE cc_start: 0.8642 (t80) cc_final: 0.8292 (t80) REVERT: V 43 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8203 (mtpt) REVERT: V 46 THR cc_start: 0.8350 (m) cc_final: 0.8078 (p) REVERT: AA 21 TYR cc_start: 0.8220 (m-10) cc_final: 0.7986 (m-80) REVERT: BA 44 LYS cc_start: 0.8467 (ttmm) cc_final: 0.8221 (ttpp) REVERT: CA 40 LYS cc_start: 0.8506 (tttt) cc_final: 0.8289 (tttt) REVERT: DA 46 THR cc_start: 0.8248 (m) cc_final: 0.7952 (p) REVERT: GA 40 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8471 (ttpp) REVERT: IA 21 TYR cc_start: 0.8326 (m-10) cc_final: 0.8103 (m-80) REVERT: LA 46 THR cc_start: 0.8212 (m) cc_final: 0.7888 (p) outliers start: 4 outliers final: 2 residues processed: 262 average time/residue: 0.3036 time to fit residues: 107.8735 Evaluate side-chains 217 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 215 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 8 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 154 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.113056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.084242 restraints weight = 16566.254| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.60 r_work: 0.3017 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3115 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= 0.153 Angle : 0.338 3.590 19000 Z= 0.202 Chirality : 0.031 0.089 2240 Planarity : 0.002 0.013 2280 Dihedral : 3.429 39.272 1920 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 1.61 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: 6.96 (0.14), residues: 1760 helix: 4.44 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 26 PHE 0.007 0.001 PHE B 45 TYR 0.011 0.002 TYR L 21 Details of bonding type rmsd hydrogen bonds : bond 0.05966 ( 1631) hydrogen bonds : angle 3.40993 ( 4893) covalent geometry : bond 0.00304 (14040) covalent geometry : angle 0.33811 (19000) *********************** 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 272 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 262 time to evaluate : 1.523 Fit side-chains REVERT: C 21 TYR cc_start: 0.8334 (m-10) cc_final: 0.8119 (m-80) REVERT: L 44 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8332 (ttpp) REVERT: F 44 LYS cc_start: 0.8276 (ttmm) cc_final: 0.8026 (tttt) REVERT: G 42 PHE cc_start: 0.8694 (t80) cc_final: 0.8422 (t80) REVERT: G 43 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8331 (mtpt) REVERT: G 46 THR cc_start: 0.8381 (m) cc_final: 0.7983 (p) REVERT: M 46 THR cc_start: 0.8340 (m) cc_final: 0.7945 (p) REVERT: Q 12 ASN cc_start: 0.8249 (m-40) cc_final: 0.7786 (m110) REVERT: V 42 PHE cc_start: 0.8609 (t80) cc_final: 0.8356 (t80) REVERT: V 43 LYS cc_start: 0.8558 (ttmm) cc_final: 0.8232 (mtpt) REVERT: V 46 THR cc_start: 0.8343 (m) cc_final: 0.8008 (p) REVERT: AA 21 TYR cc_start: 0.8298 (m-10) cc_final: 0.8088 (m-80) REVERT: BA 44 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8438 (ttpp) REVERT: DA 43 LYS cc_start: 0.8541 (ttmm) cc_final: 0.8321 (mtpt) REVERT: DA 46 THR cc_start: 0.8270 (m) cc_final: 0.7893 (p) REVERT: GA 40 LYS cc_start: 0.8937 (ttmm) cc_final: 0.8604 (ttpp) REVERT: IA 21 TYR cc_start: 0.8374 (m-10) cc_final: 0.8141 (m-80) REVERT: JA 44 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8427 (ttpp) REVERT: LA 8 LYS cc_start: 0.7640 (tttp) cc_final: 0.7379 (ttmm) REVERT: LA 46 THR cc_start: 0.8266 (m) cc_final: 0.7928 (p) outliers start: 10 outliers final: 7 residues processed: 263 average time/residue: 0.3089 time to fit residues: 110.7889 Evaluate side-chains 249 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 242 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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 60 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 V 12 ASN W 12 ASN DA 12 ASN EA 12 ASN MA 12 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.084371 restraints weight = 16478.138| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.58 r_work: 0.3110 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3452 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= 0.135 Angle : 0.313 3.441 19000 Z= 0.188 Chirality : 0.031 0.175 2240 Planarity : 0.002 0.017 2280 Dihedral : 3.239 48.376 1920 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.59 % Allowed : 10.81 % Favored : 88.60 % 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: 7.03 (0.14), residues: 1760 helix: 4.49 (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 0.006 0.001 PHE A 45 TYR 0.016 0.001 TYRHA 24 Details of bonding type rmsd hydrogen bonds : bond 0.05411 ( 1631) hydrogen bonds : angle 3.33616 ( 4893) covalent geometry : bond 0.00245 (14040) covalent geometry : angle 0.31337 (19000) *********************** 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 266 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 258 time to evaluate : 1.335 Fit side-chains REVERT: C 21 TYR cc_start: 0.8396 (m-10) cc_final: 0.8148 (m-80) REVERT: F 44 LYS cc_start: 0.8325 (ttmm) cc_final: 0.8093 (tttt) REVERT: G 46 THR cc_start: 0.8433 (m) cc_final: 0.8018 (p) REVERT: M 46 THR cc_start: 0.8185 (m) cc_final: 0.7802 (p) REVERT: Q 12 ASN cc_start: 0.8320 (m-40) cc_final: 0.8025 (m110) REVERT: S 48 LYS cc_start: 0.8397 (mmtm) cc_final: 0.8176 (mptt) REVERT: T 28 MET cc_start: 0.8930 (ttp) cc_final: 0.8647 (ttt) REVERT: V 43 LYS cc_start: 0.8529 (ttmm) cc_final: 0.8173 (mtpt) REVERT: V 46 THR cc_start: 0.8313 (m) cc_final: 0.7938 (p) REVERT: AA 21 TYR cc_start: 0.8382 (m-10) cc_final: 0.8098 (m-80) REVERT: BA 44 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8461 (ttpp) REVERT: DA 43 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8197 (mtpt) REVERT: DA 46 THR cc_start: 0.8240 (m) cc_final: 0.7841 (p) REVERT: GA 40 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8660 (ttpp) REVERT: IA 21 TYR cc_start: 0.8426 (m-10) cc_final: 0.8119 (m-80) REVERT: JA 44 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8453 (ttpp) REVERT: JA 48 LYS cc_start: 0.8240 (mttm) cc_final: 0.8001 (mmtm) REVERT: LA 8 LYS cc_start: 0.7717 (tttp) cc_final: 0.7427 (ttmm) REVERT: LA 46 THR cc_start: 0.8259 (m) cc_final: 0.7859 (p) REVERT: OA 20 GLU cc_start: 0.7919 (tt0) cc_final: 0.7588 (tt0) outliers start: 8 outliers final: 6 residues processed: 259 average time/residue: 0.3092 time to fit residues: 110.6126 Evaluate side-chains 253 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 247 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain H residue 48 LYS 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 45 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.107433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.079741 restraints weight = 16662.066| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.50 r_work: 0.2979 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14040 Z= 0.179 Angle : 0.358 3.644 19000 Z= 0.214 Chirality : 0.032 0.100 2240 Planarity : 0.002 0.021 2280 Dihedral : 3.458 44.745 1920 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.03 % Allowed : 11.62 % Favored : 87.35 % 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: 6.61 (0.15), residues: 1760 helix: 4.23 (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 0.009 0.001 PHE E 45 TYR 0.021 0.001 TYRHA 24 Details of bonding type rmsd hydrogen bonds : bond 0.06352 ( 1631) hydrogen bonds : angle 3.44920 ( 4893) covalent geometry : bond 0.00394 (14040) covalent geometry : angle 0.35780 (19000) *********************** 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 268 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 254 time to evaluate : 1.367 Fit side-chains REVERT: C 21 TYR cc_start: 0.8450 (m-10) cc_final: 0.8184 (m-80) REVERT: F 44 LYS cc_start: 0.8443 (ttmm) cc_final: 0.8194 (tttt) REVERT: G 46 THR cc_start: 0.8521 (m) cc_final: 0.8081 (p) REVERT: M 46 THR cc_start: 0.8350 (m) cc_final: 0.7957 (p) REVERT: T 28 MET cc_start: 0.8976 (ttp) cc_final: 0.8692 (ttt) REVERT: V 43 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8258 (mtpt) REVERT: V 46 THR cc_start: 0.8392 (m) cc_final: 0.8027 (p) REVERT: AA 21 TYR cc_start: 0.8436 (m-10) cc_final: 0.8114 (m-80) REVERT: BA 44 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8557 (ttpp) REVERT: DA 43 LYS cc_start: 0.8638 (ttmm) cc_final: 0.8379 (mtpp) REVERT: DA 46 THR cc_start: 0.8415 (m) cc_final: 0.7997 (p) REVERT: IA 21 TYR cc_start: 0.8500 (m-10) cc_final: 0.8182 (m-80) REVERT: LA 8 LYS cc_start: 0.7853 (tttp) cc_final: 0.7555 (ttmm) REVERT: LA 46 THR cc_start: 0.8358 (m) cc_final: 0.7953 (p) REVERT: OA 40 LYS cc_start: 0.9192 (ttpp) cc_final: 0.8944 (ttpp) outliers start: 14 outliers final: 8 residues processed: 259 average time/residue: 0.2901 time to fit residues: 103.8459 Evaluate side-chains 260 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 252 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain N residue 48 LYS Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain GA residue 47 SER Chi-restraints excluded: chain KA residue 44 LYS Chi-restraints excluded: chain OA residue 47 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.109393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.081812 restraints weight = 16793.145| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.49 r_work: 0.3009 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14040 Z= 0.151 Angle : 0.326 3.667 19000 Z= 0.196 Chirality : 0.031 0.099 2240 Planarity : 0.002 0.021 2280 Dihedral : 3.308 46.499 1920 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.81 % Allowed : 12.50 % Favored : 86.69 % 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: 6.75 (0.14), residues: 1760 helix: 4.31 (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 C 11 TYR 0.021 0.001 TYRHA 24 Details of bonding type rmsd hydrogen bonds : bond 0.05849 ( 1631) hydrogen bonds : angle 3.38230 ( 4893) covalent geometry : bond 0.00307 (14040) covalent geometry : angle 0.32640 (19000) *********************** 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 259 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 248 time to evaluate : 1.361 Fit side-chains REVERT: C 21 TYR cc_start: 0.8443 (m-10) cc_final: 0.8178 (m-80) REVERT: F 44 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8173 (tttt) REVERT: G 46 THR cc_start: 0.8492 (m) cc_final: 0.8066 (p) REVERT: M 46 THR cc_start: 0.8342 (m) cc_final: 0.7939 (p) REVERT: T 12 ASN cc_start: 0.8594 (m110) cc_final: 0.8357 (m110) REVERT: T 28 MET cc_start: 0.8949 (ttp) cc_final: 0.8682 (ttt) REVERT: V 43 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8188 (mtpt) REVERT: V 46 THR cc_start: 0.8370 (m) cc_final: 0.8012 (p) REVERT: AA 21 TYR cc_start: 0.8462 (m-10) cc_final: 0.8119 (m-80) REVERT: BA 44 LYS cc_start: 0.8828 (ttmm) cc_final: 0.8535 (ttpp) REVERT: DA 43 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8334 (mtpp) REVERT: DA 46 THR cc_start: 0.8401 (m) cc_final: 0.7965 (p) REVERT: LA 8 LYS cc_start: 0.7796 (tttp) cc_final: 0.7498 (ttmm) REVERT: LA 46 THR cc_start: 0.8320 (m) cc_final: 0.7877 (p) REVERT: OA 40 LYS cc_start: 0.9197 (ttpp) cc_final: 0.8869 (ttpp) outliers start: 11 outliers final: 8 residues processed: 251 average time/residue: 0.2841 time to fit residues: 98.2169 Evaluate side-chains 249 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 241 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 47 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 59 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 89 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.112389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.084728 restraints weight = 16550.259| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.49 r_work: 0.3128 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3763 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= 0.135 Angle : 0.309 3.538 19000 Z= 0.186 Chirality : 0.031 0.100 2240 Planarity : 0.002 0.018 2280 Dihedral : 3.103 45.582 1920 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.74 % Allowed : 12.72 % Favored : 86.54 % 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: 6.99 (0.14), residues: 1760 helix: 4.46 (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 TRPCA 26 PHE 0.008 0.001 PHE C 11 TYR 0.022 0.001 TYRHA 24 Details of bonding type rmsd hydrogen bonds : bond 0.05419 ( 1631) hydrogen bonds : angle 3.33153 ( 4893) covalent geometry : bond 0.00247 (14040) covalent geometry : angle 0.30859 (19000) *********************** 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 249 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 239 time to evaluate : 1.396 Fit side-chains REVERT: F 44 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8460 (tttt) REVERT: G 46 THR cc_start: 0.8574 (m) cc_final: 0.8131 (p) REVERT: M 46 THR cc_start: 0.8430 (m) cc_final: 0.8013 (p) REVERT: S 48 LYS cc_start: 0.8536 (mmtm) cc_final: 0.8316 (mptt) REVERT: T 28 MET cc_start: 0.8961 (ttp) cc_final: 0.8756 (ttt) REVERT: V 43 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8326 (mtpt) REVERT: V 46 THR cc_start: 0.8550 (m) cc_final: 0.8172 (p) REVERT: AA 21 TYR cc_start: 0.8474 (m-10) cc_final: 0.8099 (m-80) REVERT: BA 44 LYS cc_start: 0.9006 (ttmm) cc_final: 0.8724 (ttpp) REVERT: BA 48 LYS cc_start: 0.8484 (mttm) cc_final: 0.8028 (mtpt) REVERT: DA 43 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8435 (mtpt) REVERT: DA 46 THR cc_start: 0.8498 (m) cc_final: 0.8023 (p) REVERT: JA 44 LYS cc_start: 0.8945 (ttmm) cc_final: 0.8739 (ttpp) REVERT: LA 8 LYS cc_start: 0.7927 (tttp) cc_final: 0.7672 (ttmm) REVERT: LA 46 THR cc_start: 0.8366 (m) cc_final: 0.7916 (p) REVERT: OA 40 LYS cc_start: 0.9272 (ttpp) cc_final: 0.9044 (ttpp) outliers start: 10 outliers final: 9 residues processed: 242 average time/residue: 0.2982 time to fit residues: 98.6025 Evaluate side-chains 246 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 237 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain K residue 13 SER 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 125 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.116453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.087749 restraints weight = 16329.114| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.54 r_work: 0.3016 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14040 Z= 0.146 Angle : 0.320 3.543 19000 Z= 0.193 Chirality : 0.031 0.098 2240 Planarity : 0.002 0.018 2280 Dihedral : 3.150 45.167 1920 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.66 % Allowed : 12.94 % Favored : 86.40 % 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: 6.88 (0.14), residues: 1760 helix: 4.40 (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 0.009 0.001 PHE C 11 TYR 0.022 0.001 TYRHA 24 Details of bonding type rmsd hydrogen bonds : bond 0.05647 ( 1631) hydrogen bonds : angle 3.36260 ( 4893) covalent geometry : bond 0.00289 (14040) covalent geometry : angle 0.31953 (19000) *********************** 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 252 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 243 time to evaluate : 1.558 Fit side-chains REVERT: F 12 ASN cc_start: 0.8445 (m110) cc_final: 0.8183 (m110) REVERT: G 46 THR cc_start: 0.8442 (m) cc_final: 0.8000 (p) REVERT: S 48 LYS cc_start: 0.8335 (mmtm) cc_final: 0.8127 (mptt) REVERT: T 28 MET cc_start: 0.8911 (ttp) cc_final: 0.8660 (ttt) REVERT: V 43 LYS cc_start: 0.8456 (ttmm) cc_final: 0.8088 (mtpt) REVERT: V 46 THR cc_start: 0.8408 (m) cc_final: 0.8048 (p) REVERT: AA 21 TYR cc_start: 0.8387 (m-10) cc_final: 0.8045 (m-80) REVERT: BA 44 LYS cc_start: 0.8800 (ttmm) cc_final: 0.8535 (ttpp) REVERT: BA 48 LYS cc_start: 0.8295 (mttm) cc_final: 0.7799 (mtpt) REVERT: DA 43 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8207 (mtpt) REVERT: DA 46 THR cc_start: 0.8338 (m) cc_final: 0.7899 (p) REVERT: JA 44 LYS cc_start: 0.8735 (ttmm) cc_final: 0.8501 (ttpp) REVERT: LA 8 LYS cc_start: 0.7691 (tttp) cc_final: 0.7409 (ttmm) REVERT: LA 46 THR cc_start: 0.8195 (m) cc_final: 0.7753 (p) REVERT: OA 40 LYS cc_start: 0.9231 (ttpp) cc_final: 0.8899 (ttpp) outliers start: 9 outliers final: 8 residues processed: 246 average time/residue: 0.2914 time to fit residues: 99.0513 Evaluate side-chains 249 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 241 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain A residue 14 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 47 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 128 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 48 optimal weight: 0.0270 chunk 155 optimal weight: 0.8980 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.118744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.090041 restraints weight = 16239.735| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.54 r_work: 0.3060 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3899 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= 0.132 Angle : 0.306 3.470 19000 Z= 0.186 Chirality : 0.031 0.098 2240 Planarity : 0.002 0.017 2280 Dihedral : 2.971 43.440 1920 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.66 % Allowed : 13.09 % Favored : 86.25 % 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: 7.04 (0.14), residues: 1760 helix: 4.49 (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 0.010 0.001 PHE C 11 TYR 0.025 0.001 TYRHA 24 Details of bonding type rmsd hydrogen bonds : bond 0.05262 ( 1631) hydrogen bonds : angle 3.32216 ( 4893) covalent geometry : bond 0.00240 (14040) covalent geometry : angle 0.30602 (19000) *********************** 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 250 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 241 time to evaluate : 1.502 Fit side-chains REVERT: G 46 THR cc_start: 0.8375 (m) cc_final: 0.7942 (p) REVERT: N 8 LYS cc_start: 0.7789 (ttmm) cc_final: 0.7550 (ttpt) REVERT: T 28 MET cc_start: 0.8887 (ttp) cc_final: 0.8660 (ttt) REVERT: V 43 LYS cc_start: 0.8470 (ttmm) cc_final: 0.8098 (mtpt) REVERT: V 46 THR cc_start: 0.8404 (m) cc_final: 0.8077 (p) REVERT: AA 21 TYR cc_start: 0.8369 (m-10) cc_final: 0.8016 (m-80) REVERT: BA 44 LYS cc_start: 0.8781 (ttmm) cc_final: 0.8508 (ttpp) REVERT: BA 48 LYS cc_start: 0.8334 (mttm) cc_final: 0.7820 (mtpt) REVERT: DA 43 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8140 (mtpt) REVERT: DA 46 THR cc_start: 0.8318 (m) cc_final: 0.7879 (p) REVERT: JA 44 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8520 (ttpp) REVERT: LA 8 LYS cc_start: 0.7636 (tttp) cc_final: 0.7377 (ttmm) REVERT: LA 46 THR cc_start: 0.8179 (m) cc_final: 0.7712 (p) outliers start: 9 outliers final: 7 residues processed: 242 average time/residue: 0.3092 time to fit residues: 102.1352 Evaluate side-chains 244 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 237 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain A residue 14 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 28 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 92 optimal weight: 0.0980 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.120537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.092070 restraints weight = 16228.472| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.53 r_work: 0.3084 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4018 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= 0.126 Angle : 0.304 4.091 19000 Z= 0.185 Chirality : 0.031 0.122 2240 Planarity : 0.002 0.017 2280 Dihedral : 2.852 42.550 1920 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.37 % Allowed : 13.46 % Favored : 86.18 % 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: 4.55 (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 TRPBA 26 PHE 0.014 0.001 PHE C 11 TYR 0.027 0.001 TYR C 21 Details of bonding type rmsd hydrogen bonds : bond 0.05030 ( 1631) hydrogen bonds : angle 3.31221 ( 4893) covalent geometry : bond 0.00217 (14040) covalent geometry : angle 0.30389 (19000) ********************** 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 247 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 242 time to evaluate : 1.594 Fit side-chains REVERT: G 46 THR cc_start: 0.8357 (m) cc_final: 0.7914 (p) REVERT: N 8 LYS cc_start: 0.7775 (ttmm) cc_final: 0.7566 (ttpt) REVERT: T 28 MET cc_start: 0.8868 (ttp) cc_final: 0.8636 (ttt) REVERT: V 43 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8164 (mtpt) REVERT: V 46 THR cc_start: 0.8362 (m) cc_final: 0.8030 (p) REVERT: AA 21 TYR cc_start: 0.8343 (m-10) cc_final: 0.7982 (m-80) REVERT: BA 44 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8460 (ttpp) REVERT: BA 48 LYS cc_start: 0.8260 (mttm) cc_final: 0.7753 (mtpt) REVERT: DA 43 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8107 (mtpt) REVERT: DA 46 THR cc_start: 0.8316 (m) cc_final: 0.7876 (p) REVERT: JA 44 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8457 (ttpp) REVERT: LA 46 THR cc_start: 0.8084 (m) cc_final: 0.7631 (p) outliers start: 5 outliers final: 5 residues processed: 242 average time/residue: 0.3014 time to fit residues: 99.8211 Evaluate side-chains 243 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 238 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 EA residue 48 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 32 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.114396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.085665 restraints weight = 16450.183| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.55 r_work: 0.2989 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14040 Z= 0.163 Angle : 0.348 3.900 19000 Z= 0.210 Chirality : 0.032 0.122 2240 Planarity : 0.002 0.018 2280 Dihedral : 3.108 33.726 1920 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.44 % Allowed : 13.53 % 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: 6.72 (0.15), residues: 1760 helix: 4.30 (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 0.012 0.001 PHE C 11 TYR 0.024 0.001 TYR C 21 Details of bonding type rmsd hydrogen bonds : bond 0.05966 ( 1631) hydrogen bonds : angle 3.43964 ( 4893) covalent geometry : bond 0.00344 (14040) covalent geometry : angle 0.34752 (19000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6522.74 seconds wall clock time: 114 minutes 6.39 seconds (6846.39 seconds total)