Starting phenix.real_space_refine on Thu Jul 31 09:57:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ixj_35793/07_2025/8ixj_35793.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ixj_35793/07_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_35793/07_2025/8ixj_35793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ixj_35793/07_2025/8ixj_35793.map" model { file = "/net/cci-nas-00/data/ceres_data/8ixj_35793/07_2025/8ixj_35793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ixj_35793/07_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-5711/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: 8.07, per 1000 atoms: 0.59 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: 3.44 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: 1.10 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: 4.16 Time building geometry restraints manager: 4.04 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: 1.130 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.800 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.560 ------------------------------------------------------------------------------- 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 : 1.283 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: 0.3637 time to fit residues: 103.3993 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 : 2.191 ------------------------------------------------------------------------------- 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 = 53)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.093342 restraints weight = 16016.054| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.52 r_work: 0.3132 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 1.574 Fit side-chains REVERT: C 21 TYR cc_start: 0.8284 (m-10) cc_final: 0.8063 (m-80) REVERT: F 44 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7858 (tttt) REVERT: F 46 THR cc_start: 0.8611 (m) cc_final: 0.8363 (p) REVERT: G 46 THR cc_start: 0.8313 (m) cc_final: 0.7973 (p) REVERT: M 46 THR cc_start: 0.8324 (m) cc_final: 0.7976 (p) REVERT: P 40 LYS cc_start: 0.8796 (ttmm) cc_final: 0.8303 (ttpt) REVERT: V 42 PHE cc_start: 0.8662 (t80) cc_final: 0.8312 (t80) REVERT: V 43 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8225 (mtpt) REVERT: V 46 THR cc_start: 0.8375 (m) cc_final: 0.8101 (p) REVERT: AA 21 TYR cc_start: 0.8229 (m-10) cc_final: 0.7991 (m-80) REVERT: BA 44 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8216 (ttpp) REVERT: CA 40 LYS cc_start: 0.8503 (tttt) cc_final: 0.8286 (tttt) REVERT: DA 46 THR cc_start: 0.8280 (m) cc_final: 0.7982 (p) REVERT: GA 40 LYS cc_start: 0.8781 (ttmm) cc_final: 0.8468 (ttpp) REVERT: IA 21 TYR cc_start: 0.8334 (m-10) cc_final: 0.8107 (m-80) REVERT: LA 46 THR cc_start: 0.8243 (m) cc_final: 0.7917 (p) outliers start: 4 outliers final: 2 residues processed: 262 average time/residue: 0.3379 time to fit residues: 120.4221 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 : 1.479 ------------------------------------------------------------------------------- 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: 0.9980 chunk 73 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.110138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.081574 restraints weight = 16733.863| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.59 r_work: 0.3064 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 14040 Z= 0.155 Angle : 0.340 3.608 19000 Z= 0.203 Chirality : 0.031 0.091 2240 Planarity : 0.002 0.013 2280 Dihedral : 3.455 39.489 1920 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.66 % Allowed : 10.00 % Favored : 89.34 % 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: 6.93 (0.14), residues: 1760 helix: 4.42 (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 0.06002 ( 1631) hydrogen bonds : angle 3.41821 ( 4893) covalent geometry : bond 0.00307 (14040) covalent geometry : angle 0.33989 (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 275 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 266 time to evaluate : 1.646 Fit side-chains REVERT: C 21 TYR cc_start: 0.8388 (m-10) cc_final: 0.8151 (m-80) REVERT: L 44 LYS cc_start: 0.8790 (ttmm) cc_final: 0.8536 (ttpp) REVERT: F 44 LYS cc_start: 0.8504 (ttmm) cc_final: 0.8262 (tttt) REVERT: G 42 PHE cc_start: 0.8807 (t80) cc_final: 0.8535 (t80) REVERT: G 43 LYS cc_start: 0.8657 (ttmm) cc_final: 0.8454 (mtpt) REVERT: G 46 THR cc_start: 0.8459 (m) cc_final: 0.8052 (p) REVERT: M 46 THR cc_start: 0.8418 (m) cc_final: 0.8016 (p) REVERT: Q 12 ASN cc_start: 0.8301 (m-40) cc_final: 0.7838 (m110) REVERT: V 42 PHE cc_start: 0.8733 (t80) cc_final: 0.8481 (t80) REVERT: V 43 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8368 (mtpt) REVERT: V 46 THR cc_start: 0.8432 (m) cc_final: 0.8088 (p) REVERT: AA 21 TYR cc_start: 0.8374 (m-10) cc_final: 0.8134 (m-80) REVERT: BA 44 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8637 (ttpp) REVERT: DA 46 THR cc_start: 0.8349 (m) cc_final: 0.7966 (p) REVERT: GA 40 LYS cc_start: 0.9059 (ttmm) cc_final: 0.8766 (ttpp) REVERT: IA 21 TYR cc_start: 0.8431 (m-10) cc_final: 0.8173 (m-80) REVERT: JA 44 LYS cc_start: 0.8880 (ttmm) cc_final: 0.8644 (ttpp) REVERT: LA 8 LYS cc_start: 0.7824 (tttp) cc_final: 0.7575 (ttmm) REVERT: LA 46 THR cc_start: 0.8359 (m) cc_final: 0.8009 (p) outliers start: 9 outliers final: 7 residues processed: 267 average time/residue: 0.3849 time to fit residues: 139.7975 Evaluate side-chains 252 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 245 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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 CA 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: 1.9990 chunk 93 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 63 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 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 = 0.3605 r_free = 0.3605 target = 0.112371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.083739 restraints weight = 16570.722| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.59 r_work: 0.3038 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14040 Z= 0.141 Angle : 0.319 3.478 19000 Z= 0.191 Chirality : 0.031 0.110 2240 Planarity : 0.002 0.018 2280 Dihedral : 3.326 48.457 1920 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.74 % Allowed : 10.88 % Favored : 88.38 % 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: 6.95 (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 0.005 0.001 TRP V 26 PHE 0.007 0.001 PHE E 45 TYR 0.016 0.001 TYRHA 24 Details of bonding type rmsd hydrogen bonds : bond 0.05570 ( 1631) hydrogen bonds : angle 3.36034 ( 4893) covalent geometry : bond 0.00268 (14040) covalent geometry : angle 0.31928 (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 262 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 252 time to evaluate : 1.500 Fit side-chains REVERT: C 21 TYR cc_start: 0.8383 (m-10) cc_final: 0.8147 (m-80) REVERT: L 44 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8360 (ttpp) REVERT: F 12 ASN cc_start: 0.8550 (m110) cc_final: 0.8338 (m110) REVERT: F 44 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7998 (tttt) REVERT: G 46 THR cc_start: 0.8376 (m) cc_final: 0.7966 (p) REVERT: M 46 THR cc_start: 0.8118 (m) cc_final: 0.7736 (p) REVERT: Q 12 ASN cc_start: 0.8299 (m-40) cc_final: 0.7985 (m110) REVERT: T 28 MET cc_start: 0.8921 (ttp) cc_final: 0.8621 (ttt) REVERT: V 43 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8083 (mtpt) REVERT: V 46 THR cc_start: 0.8261 (m) cc_final: 0.7890 (p) REVERT: Y 40 LYS cc_start: 0.9207 (ttpp) cc_final: 0.8974 (ttpp) REVERT: AA 21 TYR cc_start: 0.8352 (m-10) cc_final: 0.8084 (m-80) REVERT: BA 44 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8399 (ttpp) REVERT: DA 46 THR cc_start: 0.8193 (m) cc_final: 0.7791 (p) REVERT: IA 21 TYR cc_start: 0.8407 (m-10) cc_final: 0.8116 (m-80) REVERT: JA 44 LYS cc_start: 0.8662 (ttmm) cc_final: 0.8413 (ttpp) REVERT: LA 8 LYS cc_start: 0.7674 (tttp) cc_final: 0.7385 (ttmm) REVERT: LA 46 THR cc_start: 0.8174 (m) cc_final: 0.7789 (p) REVERT: OA 40 LYS cc_start: 0.9192 (ttpp) cc_final: 0.8983 (ttpt) outliers start: 10 outliers final: 8 residues processed: 254 average time/residue: 0.3540 time to fit residues: 124.7801 Evaluate side-chains 255 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 247 time to evaluate : 1.833 ------------------------------------------------------------------------------- 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 CA residue 47 SER 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=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: 0.9980 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DA 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.107643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.080138 restraints weight = 16548.583| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.50 r_work: 0.3001 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14040 Z= 0.172 Angle : 0.350 3.624 19000 Z= 0.209 Chirality : 0.032 0.097 2240 Planarity : 0.002 0.021 2280 Dihedral : 3.456 45.015 1920 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.96 % Allowed : 11.54 % Favored : 87.50 % 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: 6.64 (0.14), residues: 1760 helix: 4.25 (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 0.008 0.001 PHE E 45 TYR 0.021 0.001 TYRHA 24 Details of bonding type rmsd hydrogen bonds : bond 0.06206 ( 1631) hydrogen bonds : angle 3.43993 ( 4893) covalent geometry : bond 0.00373 (14040) covalent geometry : angle 0.35001 (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 274 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 261 time to evaluate : 1.430 Fit side-chains REVERT: C 21 TYR cc_start: 0.8459 (m-10) cc_final: 0.8195 (m-80) REVERT: L 44 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8521 (ttpp) REVERT: F 44 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8208 (tttt) REVERT: G 46 THR cc_start: 0.8524 (m) cc_final: 0.8080 (p) REVERT: M 46 THR cc_start: 0.8355 (m) cc_final: 0.7957 (p) REVERT: T 28 MET cc_start: 0.8967 (ttp) cc_final: 0.8683 (ttt) REVERT: V 43 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8275 (mtpt) REVERT: V 46 THR cc_start: 0.8401 (m) cc_final: 0.8035 (p) REVERT: AA 21 TYR cc_start: 0.8476 (m-10) cc_final: 0.8134 (m-80) REVERT: BA 44 LYS cc_start: 0.8872 (ttmm) cc_final: 0.8591 (ttpp) REVERT: DA 46 THR cc_start: 0.8378 (m) cc_final: 0.7962 (p) REVERT: IA 21 TYR cc_start: 0.8501 (m-10) cc_final: 0.8179 (m-80) REVERT: LA 8 LYS cc_start: 0.7862 (tttp) cc_final: 0.7559 (ttmm) REVERT: LA 46 THR cc_start: 0.8379 (m) cc_final: 0.7983 (p) outliers start: 13 outliers final: 8 residues processed: 264 average time/residue: 0.3249 time to fit residues: 119.3876 Evaluate side-chains 262 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 254 time to evaluate : 1.819 ------------------------------------------------------------------------------- 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 P residue 47 SER Chi-restraints excluded: chain CA 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: 0.9990 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: 8.9990 chunk 65 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DA 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.111089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.083677 restraints weight = 16639.789| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.48 r_work: 0.3032 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14040 Z= 0.142 Angle : 0.316 3.489 19000 Z= 0.190 Chirality : 0.031 0.098 2240 Planarity : 0.002 0.021 2280 Dihedral : 3.206 47.671 1920 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.81 % Allowed : 12.43 % 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: 6.87 (0.14), residues: 1760 helix: 4.39 (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 TRPCA 26 PHE 0.006 0.001 PHE C 11 TYR 0.021 0.001 TYRHA 24 Details of bonding type rmsd hydrogen bonds : bond 0.05601 ( 1631) hydrogen bonds : angle 3.35687 ( 4893) covalent geometry : bond 0.00273 (14040) covalent geometry : angle 0.31580 (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 261 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 250 time to evaluate : 1.577 Fit side-chains REVERT: F 12 ASN cc_start: 0.8621 (m110) cc_final: 0.8417 (m110) REVERT: F 44 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8220 (tttt) REVERT: G 46 THR cc_start: 0.8517 (m) cc_final: 0.8083 (p) REVERT: M 46 THR cc_start: 0.8358 (m) cc_final: 0.7950 (p) REVERT: S 48 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8149 (mptt) REVERT: T 12 ASN cc_start: 0.8603 (m110) cc_final: 0.8382 (m110) REVERT: T 28 MET cc_start: 0.8935 (ttp) cc_final: 0.8693 (ttt) REVERT: V 43 LYS cc_start: 0.8561 (ttmm) cc_final: 0.8225 (mtpt) REVERT: V 46 THR cc_start: 0.8388 (m) cc_final: 0.8026 (p) REVERT: AA 21 TYR cc_start: 0.8456 (m-10) cc_final: 0.8104 (m-80) REVERT: BA 44 LYS cc_start: 0.8804 (ttmm) cc_final: 0.8500 (ttpp) REVERT: DA 46 THR cc_start: 0.8404 (m) cc_final: 0.7959 (p) REVERT: JA 44 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8557 (ttpp) REVERT: LA 8 LYS cc_start: 0.7778 (tttp) cc_final: 0.7485 (ttmm) REVERT: LA 46 THR cc_start: 0.8344 (m) cc_final: 0.7895 (p) outliers start: 11 outliers final: 8 residues processed: 253 average time/residue: 0.3142 time to fit residues: 108.3094 Evaluate side-chains 253 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 245 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 CA residue 47 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 59 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 131 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 136 optimal weight: 0.4980 chunk 157 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 12 ASN V 12 ASN DA 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.116679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.089007 restraints weight = 16449.432| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.50 r_work: 0.3169 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14040 Z= 0.119 Angle : 0.290 3.462 19000 Z= 0.175 Chirality : 0.031 0.111 2240 Planarity : 0.002 0.018 2280 Dihedral : 2.840 46.222 1920 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.51 % Allowed : 13.01 % Favored : 86.47 % 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: 7.28 (0.14), residues: 1760 helix: 4.64 (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 TRPMA 26 PHE 0.007 0.001 PHE C 11 TYR 0.021 0.001 TYRHA 24 Details of bonding type rmsd hydrogen bonds : bond 0.04826 ( 1631) hydrogen bonds : angle 3.24351 ( 4893) covalent geometry : bond 0.00195 (14040) covalent geometry : angle 0.29010 (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 258 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 251 time to evaluate : 1.574 Fit side-chains REVERT: G 46 THR cc_start: 0.8549 (m) cc_final: 0.8104 (p) REVERT: N 8 LYS cc_start: 0.7826 (ttmm) cc_final: 0.7621 (ttpt) REVERT: V 43 LYS cc_start: 0.8657 (ttmm) cc_final: 0.8305 (mtpt) REVERT: V 46 THR cc_start: 0.8511 (m) cc_final: 0.8147 (p) REVERT: AA 21 TYR cc_start: 0.8438 (m-10) cc_final: 0.8049 (m-80) REVERT: BA 44 LYS cc_start: 0.8937 (ttmm) cc_final: 0.8688 (ttpp) REVERT: DA 46 THR cc_start: 0.8483 (m) cc_final: 0.8023 (p) REVERT: JA 44 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8677 (ttpp) REVERT: LA 46 THR cc_start: 0.8345 (m) cc_final: 0.7873 (p) outliers start: 7 outliers final: 6 residues processed: 251 average time/residue: 0.3220 time to fit residues: 110.2150 Evaluate side-chains 245 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 239 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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 HA residue 28 MET 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 125 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 V 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.112388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.083801 restraints weight = 16447.206| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.56 r_work: 0.2963 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14040 Z= 0.192 Angle : 0.368 3.725 19000 Z= 0.221 Chirality : 0.033 0.106 2240 Planarity : 0.002 0.018 2280 Dihedral : 3.326 40.476 1920 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.10 % Allowed : 13.16 % Favored : 85.74 % 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: 6.65 (0.15), residues: 1760 helix: 4.25 (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 TRPDA 26 PHE 0.009 0.001 PHE E 45 TYR 0.024 0.002 TYRHA 24 Details of bonding type rmsd hydrogen bonds : bond 0.06398 ( 1631) hydrogen bonds : angle 3.47022 ( 4893) covalent geometry : bond 0.00438 (14040) covalent geometry : angle 0.36844 (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 271 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 256 time to evaluate : 1.538 Fit side-chains REVERT: C 21 TYR cc_start: 0.8444 (m-10) cc_final: 0.8239 (m-80) REVERT: G 46 THR cc_start: 0.8479 (m) cc_final: 0.8059 (p) REVERT: M 46 THR cc_start: 0.8235 (m) cc_final: 0.7835 (p) REVERT: V 43 LYS cc_start: 0.8468 (ttmm) cc_final: 0.8110 (mtpt) REVERT: V 46 THR cc_start: 0.8448 (m) cc_final: 0.8073 (p) REVERT: AA 21 TYR cc_start: 0.8402 (m-10) cc_final: 0.8059 (m-80) REVERT: BA 44 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8542 (ttpp) REVERT: DA 46 THR cc_start: 0.8343 (m) cc_final: 0.7894 (p) REVERT: LA 46 THR cc_start: 0.8229 (m) cc_final: 0.7806 (p) outliers start: 15 outliers final: 10 residues processed: 261 average time/residue: 0.3002 time to fit residues: 107.8539 Evaluate side-chains 262 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 252 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain K residue 13 SER Chi-restraints excluded: chain N residue 48 LYS Chi-restraints excluded: chain T residue 47 SER Chi-restraints excluded: chain GA residue 47 SER Chi-restraints excluded: chain HA residue 28 MET Chi-restraints excluded: chain NA residue 44 LYS 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 47 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 41 optimal weight: 0.2980 chunk 82 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.119870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.091396 restraints weight = 16194.563| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.54 r_work: 0.3199 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3999 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 : 0.299 3.400 19000 Z= 0.183 Chirality : 0.031 0.094 2240 Planarity : 0.002 0.017 2280 Dihedral : 2.872 39.472 1920 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.74 % Allowed : 13.53 % Favored : 85.74 % 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 0.004 0.000 TRPFA 26 PHE 0.008 0.001 PHE Z 11 TYR 0.025 0.001 TYRHA 24 Details of bonding type rmsd hydrogen bonds : bond 0.05064 ( 1631) hydrogen bonds : angle 3.29815 ( 4893) covalent geometry : bond 0.00213 (14040) covalent geometry : angle 0.29939 (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 255 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 245 time to evaluate : 1.901 Fit side-chains REVERT: G 46 THR cc_start: 0.8535 (m) cc_final: 0.8086 (p) REVERT: N 8 LYS cc_start: 0.7870 (ttmm) cc_final: 0.7629 (ttpt) REVERT: V 43 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8368 (mtpt) REVERT: V 46 THR cc_start: 0.8546 (m) cc_final: 0.8214 (p) REVERT: AA 21 TYR cc_start: 0.8446 (m-10) cc_final: 0.8032 (m-80) REVERT: BA 44 LYS cc_start: 0.9027 (ttmm) cc_final: 0.8702 (ttpp) REVERT: DA 46 THR cc_start: 0.8502 (m) cc_final: 0.8034 (p) REVERT: JA 44 LYS cc_start: 0.8992 (ttmm) cc_final: 0.8778 (ttpp) REVERT: LA 46 THR cc_start: 0.8309 (m) cc_final: 0.7829 (p) outliers start: 10 outliers final: 9 residues processed: 246 average time/residue: 0.3776 time to fit residues: 127.2491 Evaluate side-chains 248 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 239 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain J residue 47 SER 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 HA residue 28 MET 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 28 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 92 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.118776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.090142 restraints weight = 16272.304| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.55 r_work: 0.3075 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4023 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= 0.128 Angle : 0.303 3.477 19000 Z= 0.185 Chirality : 0.031 0.114 2240 Planarity : 0.002 0.017 2280 Dihedral : 2.812 38.506 1920 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.66 % Allowed : 13.53 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 7.15 (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 0.000 TRPDA 26 PHE 0.013 0.001 PHE C 11 TYR 0.024 0.001 TYRHA 24 Details of bonding type rmsd hydrogen bonds : bond 0.05074 ( 1631) hydrogen bonds : angle 3.30130 ( 4893) covalent geometry : bond 0.00222 (14040) covalent geometry : angle 0.30259 (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 249 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 240 time to evaluate : 3.231 Fit side-chains REVERT: C 21 TYR cc_start: 0.8393 (m-10) cc_final: 0.8175 (m-80) REVERT: G 46 THR cc_start: 0.8353 (m) cc_final: 0.7908 (p) REVERT: N 8 LYS cc_start: 0.7783 (ttmm) cc_final: 0.7576 (ttpt) REVERT: V 43 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8157 (mtpt) REVERT: V 46 THR cc_start: 0.8359 (m) cc_final: 0.8033 (p) REVERT: AA 21 TYR cc_start: 0.8330 (m-10) cc_final: 0.7953 (m-80) REVERT: BA 44 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8434 (ttpp) REVERT: DA 46 THR cc_start: 0.8342 (m) cc_final: 0.7905 (p) REVERT: JA 44 LYS cc_start: 0.8669 (ttmm) cc_final: 0.8440 (ttpp) REVERT: LA 46 THR cc_start: 0.8086 (m) cc_final: 0.7638 (p) outliers start: 9 outliers final: 9 residues processed: 240 average time/residue: 0.5197 time to fit residues: 171.8494 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 : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain J residue 47 SER 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 X residue 36 THR Chi-restraints excluded: chain EA residue 48 LYS Chi-restraints excluded: chain GA residue 47 SER 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 32 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 24 optimal weight: 0.0370 chunk 22 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 0.0270 chunk 122 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 12 ASN V 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.122488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.094038 restraints weight = 16348.333| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.54 r_work: 0.3114 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 14040 Z= 0.121 Angle : 0.297 4.013 19000 Z= 0.182 Chirality : 0.031 0.131 2240 Planarity : 0.002 0.017 2280 Dihedral : 2.689 35.838 1920 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.81 % Allowed : 13.68 % Favored : 85.51 % 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: 7.26 (0.14), residues: 1760 helix: 4.63 (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 TRP M 26 PHE 0.013 0.001 PHE C 11 TYR 0.023 0.001 TYRHA 24 Details of bonding type rmsd hydrogen bonds : bond 0.04802 ( 1631) hydrogen bonds : angle 3.27171 ( 4893) covalent geometry : bond 0.00200 (14040) covalent geometry : angle 0.29738 (19000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7249.67 seconds wall clock time: 130 minutes 45.48 seconds (7845.48 seconds total)