Starting phenix.real_space_refine on Wed Feb 14 21:39:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cky_16706/02_2024/8cky_16706.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cky_16706/02_2024/8cky_16706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cky_16706/02_2024/8cky_16706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cky_16706/02_2024/8cky_16706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cky_16706/02_2024/8cky_16706.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cky_16706/02_2024/8cky_16706.pdb" } resolution = 2.6 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= 0.030 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 72 5.16 5 C 6546 2.51 5 N 1788 2.21 5 O 1932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10338 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1647 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 76 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "C" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1647 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 76 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "E" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1647 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 76 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "G" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1647 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 76 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "I" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1647 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 22 Chain: "J" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 76 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "K" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1647 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 22 Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 76 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Time building chain proxies: 5.47, per 1000 atoms: 0.53 Number of scatterers: 10338 At special positions: 0 Unit cell: (110.67, 112.53, 72.54, 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 72 16.00 O 1932 8.00 N 1788 7.00 C 6546 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 1.7 seconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 70.1% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.746A pdb=" N VAL A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 146 removed outlier: 3.729A pdb=" N LYS A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.219A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.679A pdb=" N LEU A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 59 removed outlier: 3.746A pdb=" N VAL C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 146 removed outlier: 3.729A pdb=" N LYS C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.219A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.679A pdb=" N LEU C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 59 removed outlier: 3.746A pdb=" N VAL E 59 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 119 Processing helix chain 'E' and resid 125 through 146 removed outlier: 3.729A pdb=" N LYS E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.219A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 3.679A pdb=" N LEU E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'G' and resid 16 through 31 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 59 removed outlier: 3.746A pdb=" N VAL G 59 " --> pdb=" O MET G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 119 Processing helix chain 'G' and resid 125 through 146 removed outlier: 3.729A pdb=" N LYS G 140 " --> pdb=" O LEU G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 160 through 176 Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.219A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.679A pdb=" N LEU G 205 " --> pdb=" O ILE G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 218 Processing helix chain 'I' and resid 16 through 31 Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 48 through 59 removed outlier: 3.746A pdb=" N VAL I 59 " --> pdb=" O MET I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 84 Processing helix chain 'I' and resid 100 through 105 Processing helix chain 'I' and resid 110 through 119 Processing helix chain 'I' and resid 125 through 146 removed outlier: 3.729A pdb=" N LYS I 140 " --> pdb=" O LEU I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'I' and resid 160 through 176 Processing helix chain 'I' and resid 178 through 193 removed outlier: 4.219A pdb=" N LEU I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL I 191 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 3.679A pdb=" N LEU I 205 " --> pdb=" O ILE I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 218 Processing helix chain 'K' and resid 16 through 31 Processing helix chain 'K' and resid 35 through 44 Processing helix chain 'K' and resid 48 through 59 removed outlier: 3.746A pdb=" N VAL K 59 " --> pdb=" O MET K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 84 Processing helix chain 'K' and resid 100 through 105 Processing helix chain 'K' and resid 110 through 119 Processing helix chain 'K' and resid 125 through 146 removed outlier: 3.729A pdb=" N LYS K 140 " --> pdb=" O LEU K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 153 Processing helix chain 'K' and resid 160 through 176 Processing helix chain 'K' and resid 178 through 193 removed outlier: 4.219A pdb=" N LEU K 190 " --> pdb=" O THR K 186 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 205 removed outlier: 3.679A pdb=" N LEU K 205 " --> pdb=" O ILE K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 218 Processing sheet with id= 1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id= 2, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= 3, first strand: chain 'E' and resid 2 through 4 Processing sheet with id= 4, first strand: chain 'G' and resid 2 through 4 Processing sheet with id= 5, first strand: chain 'I' and resid 2 through 4 Processing sheet with id= 6, first strand: chain 'K' and resid 2 through 4 642 hydrogen bonds defined for protein. 1890 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: 2.62 Time building geometry restraints manager: 4.11 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: 3420 1.34 - 1.46: 1176 1.46 - 1.58: 5838 1.58 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 10566 Sorted by residual: bond pdb=" CB PRO E 1 " pdb=" CG PRO E 1 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.06e+00 bond pdb=" CB PRO K 1 " pdb=" CG PRO K 1 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.06e+00 bond pdb=" CB PRO C 1 " pdb=" CG PRO C 1 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.05e+00 bond pdb=" CB PRO I 1 " pdb=" CG PRO I 1 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.05e+00 bond pdb=" CB PRO A 1 " pdb=" CG PRO A 1 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.04e+00 ... (remaining 10561 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.13: 516 107.13 - 113.87: 5932 113.87 - 120.60: 4076 120.60 - 127.34: 3656 127.34 - 134.07: 184 Bond angle restraints: 14364 Sorted by residual: angle pdb=" CA GLN I 176 " pdb=" CB GLN I 176 " pdb=" CG GLN I 176 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.60e+00 angle pdb=" CA GLN C 176 " pdb=" CB GLN C 176 " pdb=" CG GLN C 176 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.60e+00 angle pdb=" CA GLN K 176 " pdb=" CB GLN K 176 " pdb=" CG GLN K 176 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.60e+00 angle pdb=" CA GLN E 176 " pdb=" CB GLN E 176 " pdb=" CG GLN E 176 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.60e+00 angle pdb=" CA GLN G 176 " pdb=" CB GLN G 176 " pdb=" CG GLN G 176 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.60e+00 ... (remaining 14359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 5952 16.27 - 32.54: 336 32.54 - 48.81: 66 48.81 - 65.08: 36 65.08 - 81.35: 12 Dihedral angle restraints: 6402 sinusoidal: 2544 harmonic: 3858 Sorted by residual: dihedral pdb=" CA PHE C 32 " pdb=" C PHE C 32 " pdb=" N SER C 33 " pdb=" CA SER C 33 " ideal model delta harmonic sigma weight residual 180.00 152.06 27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA PHE I 32 " pdb=" C PHE I 32 " pdb=" N SER I 33 " pdb=" CA SER I 33 " ideal model delta harmonic sigma weight residual 180.00 152.06 27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA PHE G 32 " pdb=" C PHE G 32 " pdb=" N SER G 33 " pdb=" CA SER G 33 " ideal model delta harmonic sigma weight residual 180.00 152.06 27.94 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 6399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 988 0.037 - 0.073: 462 0.073 - 0.109: 130 0.109 - 0.146: 40 0.146 - 0.182: 12 Chirality restraints: 1632 Sorted by residual: chirality pdb=" CA GLN E 176 " pdb=" N GLN E 176 " pdb=" C GLN E 176 " pdb=" CB GLN E 176 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA GLN K 176 " pdb=" N GLN K 176 " pdb=" C GLN K 176 " pdb=" CB GLN K 176 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA GLN C 176 " pdb=" N GLN C 176 " pdb=" C GLN C 176 " pdb=" CB GLN C 176 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.26e-01 ... (remaining 1629 not shown) Planarity restraints: 1854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 132 " 0.198 9.50e-02 1.11e+02 8.90e-02 4.87e+00 pdb=" NE ARG E 132 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG E 132 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG E 132 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 132 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 132 " -0.198 9.50e-02 1.11e+02 8.90e-02 4.87e+00 pdb=" NE ARG K 132 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG K 132 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG K 132 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG K 132 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 132 " 0.198 9.50e-02 1.11e+02 8.89e-02 4.87e+00 pdb=" NE ARG I 132 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG I 132 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG I 132 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG I 132 " 0.006 2.00e-02 2.50e+03 ... (remaining 1851 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 24 2.53 - 3.12: 8088 3.12 - 3.71: 16804 3.71 - 4.31: 24528 4.31 - 4.90: 39408 Nonbonded interactions: 88852 Sorted by model distance: nonbonded pdb=" CB ALA I 14 " pdb=" OE1 GLU K 45 " model vdw 1.934 3.460 nonbonded pdb=" CB ALA C 14 " pdb=" OE1 GLU E 45 " model vdw 1.934 3.460 nonbonded pdb=" CB ALA G 14 " pdb=" OE1 GLU I 45 " model vdw 1.935 3.460 nonbonded pdb=" CB ALA A 14 " pdb=" OE1 GLU C 45 " model vdw 1.935 3.460 nonbonded pdb=" OE1 GLU A 45 " pdb=" CB ALA K 14 " model vdw 1.935 3.460 ... (remaining 88847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } 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: 3.050 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: 12.250 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 27.970 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 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:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 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 : 0.004 0.072 10566 Z= 0.270 Angle : 0.819 5.138 14364 Z= 0.485 Chirality : 0.047 0.182 1632 Planarity : 0.009 0.089 1854 Dihedral : 12.580 81.351 3894 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.54 % Allowed : 0.00 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.20 (0.21), residues: 1308 helix: 0.04 (0.15), residues: 876 sheet: -2.54 (0.33), residues: 54 loop : 1.35 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.005 TRP G 184 HIS 0.009 0.003 HIS I 12 PHE 0.013 0.003 PHE G 40 TYR 0.017 0.004 TYR E 169 ARG 0.015 0.002 ARG K 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 348 time to evaluate : 1.192 Fit side-chains REVERT: A 18 ARG cc_start: 0.7334 (ttp-170) cc_final: 0.6982 (ttt-90) REVERT: A 25 LYS cc_start: 0.7968 (mttt) cc_final: 0.7429 (mttp) REVERT: A 51 ASP cc_start: 0.8303 (m-30) cc_final: 0.7870 (m-30) REVERT: A 145 TYR cc_start: 0.8198 (m-80) cc_final: 0.7973 (m-10) REVERT: A 175 GLU cc_start: 0.7202 (tt0) cc_final: 0.6954 (mt-10) REVERT: A 187 GLU cc_start: 0.6583 (mt-10) cc_final: 0.6353 (pt0) REVERT: C 25 LYS cc_start: 0.8017 (mttt) cc_final: 0.7401 (mttp) REVERT: C 39 MET cc_start: 0.8325 (tpt) cc_final: 0.8107 (tpp) REVERT: C 51 ASP cc_start: 0.8363 (m-30) cc_final: 0.7958 (m-30) REVERT: C 66 MET cc_start: 0.8510 (mmm) cc_final: 0.8211 (mmm) REVERT: C 118 MET cc_start: 0.8752 (mtp) cc_final: 0.8410 (mtp) REVERT: C 175 GLU cc_start: 0.7197 (tt0) cc_final: 0.6928 (mt-10) REVERT: E 25 LYS cc_start: 0.8040 (mttt) cc_final: 0.7755 (ttmm) REVERT: E 103 ASP cc_start: 0.8244 (m-30) cc_final: 0.8012 (m-30) REVERT: E 144 MET cc_start: 0.8073 (ttm) cc_final: 0.7850 (ttp) REVERT: E 175 GLU cc_start: 0.7172 (tt0) cc_final: 0.6904 (mm-30) REVERT: E 187 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6375 (pt0) REVERT: G 18 ARG cc_start: 0.7334 (ttp-170) cc_final: 0.6961 (ttt-90) REVERT: G 25 LYS cc_start: 0.7965 (mttt) cc_final: 0.7427 (mttp) REVERT: G 51 ASP cc_start: 0.8304 (m-30) cc_final: 0.7871 (m-30) REVERT: G 145 TYR cc_start: 0.8201 (m-80) cc_final: 0.7975 (m-10) REVERT: G 175 GLU cc_start: 0.7208 (tt0) cc_final: 0.6956 (mt-10) REVERT: G 187 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6351 (pt0) REVERT: I 25 LYS cc_start: 0.8017 (mttt) cc_final: 0.7401 (mttp) REVERT: I 39 MET cc_start: 0.8326 (tpt) cc_final: 0.8109 (tpp) REVERT: I 51 ASP cc_start: 0.8364 (m-30) cc_final: 0.7957 (m-30) REVERT: I 66 MET cc_start: 0.8513 (mmm) cc_final: 0.8212 (mmm) REVERT: I 118 MET cc_start: 0.8752 (mtp) cc_final: 0.8410 (mtp) REVERT: I 175 GLU cc_start: 0.7195 (tt0) cc_final: 0.6925 (mt-10) REVERT: K 25 LYS cc_start: 0.8038 (mttt) cc_final: 0.7753 (ttmm) REVERT: K 103 ASP cc_start: 0.8242 (m-30) cc_final: 0.8012 (m-30) REVERT: K 144 MET cc_start: 0.8076 (ttm) cc_final: 0.7853 (ttp) REVERT: K 175 GLU cc_start: 0.7173 (tt0) cc_final: 0.6903 (mm-30) REVERT: K 187 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6374 (pt0) outliers start: 6 outliers final: 0 residues processed: 348 average time/residue: 1.3170 time to fit residues: 488.4794 Evaluate side-chains 290 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 0.0270 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 53 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 0.3980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 112 GLN A 193 ASN C 21 ASN C 112 GLN C 192 GLN C 219 GLN E 21 ASN E 112 GLN E 192 GLN E 193 ASN E 219 GLN G 50 GLN G 112 GLN G 193 ASN I 21 ASN I 112 GLN I 192 GLN I 219 GLN K 21 ASN K 112 GLN K 192 GLN K 193 ASN K 219 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10566 Z= 0.209 Angle : 0.502 6.085 14364 Z= 0.256 Chirality : 0.040 0.133 1632 Planarity : 0.004 0.031 1854 Dihedral : 4.581 21.591 1410 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.08 % Allowed : 11.59 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.89 (0.22), residues: 1308 helix: 1.73 (0.17), residues: 894 sheet: -1.37 (0.45), residues: 54 loop : 0.66 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 117 HIS 0.002 0.001 HIS C 84 PHE 0.010 0.002 PHE A 32 TYR 0.007 0.001 TYR G 169 ARG 0.002 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 312 time to evaluate : 1.175 Fit side-chains REVERT: A 18 ARG cc_start: 0.7196 (ttp-170) cc_final: 0.6947 (ttt-90) REVERT: A 51 ASP cc_start: 0.8170 (m-30) cc_final: 0.7970 (m-30) REVERT: A 145 TYR cc_start: 0.8142 (m-80) cc_final: 0.7913 (m-10) REVERT: A 187 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6374 (pt0) REVERT: C 25 LYS cc_start: 0.7972 (mttt) cc_final: 0.7749 (ttmm) REVERT: C 51 ASP cc_start: 0.8191 (m-30) cc_final: 0.7718 (m-30) REVERT: C 66 MET cc_start: 0.8603 (mmm) cc_final: 0.8365 (mmt) REVERT: C 118 MET cc_start: 0.8746 (mtp) cc_final: 0.8474 (mtp) REVERT: C 192 GLN cc_start: 0.7647 (tp40) cc_final: 0.7332 (tm-30) REVERT: C 212 GLU cc_start: 0.7059 (tt0) cc_final: 0.6645 (tt0) REVERT: E 51 ASP cc_start: 0.8245 (m-30) cc_final: 0.7851 (m-30) REVERT: E 136 LEU cc_start: 0.8517 (mp) cc_final: 0.8288 (mt) REVERT: E 175 GLU cc_start: 0.7089 (tt0) cc_final: 0.6885 (mt-10) REVERT: E 187 GLU cc_start: 0.6506 (mt-10) cc_final: 0.6225 (pt0) REVERT: E 192 GLN cc_start: 0.7673 (tp40) cc_final: 0.7412 (tm-30) REVERT: G 18 ARG cc_start: 0.7185 (ttp-170) cc_final: 0.6918 (ttt-90) REVERT: G 51 ASP cc_start: 0.8169 (m-30) cc_final: 0.7967 (m-30) REVERT: G 145 TYR cc_start: 0.8141 (m-80) cc_final: 0.7912 (m-10) REVERT: G 187 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6374 (pt0) REVERT: I 25 LYS cc_start: 0.7973 (mttt) cc_final: 0.7751 (ttmm) REVERT: I 51 ASP cc_start: 0.8191 (m-30) cc_final: 0.7720 (m-30) REVERT: I 66 MET cc_start: 0.8604 (mmm) cc_final: 0.8364 (mmt) REVERT: I 118 MET cc_start: 0.8746 (mtp) cc_final: 0.8474 (mtp) REVERT: I 192 GLN cc_start: 0.7642 (tp40) cc_final: 0.7331 (tm-30) REVERT: I 212 GLU cc_start: 0.7060 (tt0) cc_final: 0.6647 (tt0) REVERT: K 51 ASP cc_start: 0.8243 (m-30) cc_final: 0.7848 (m-30) REVERT: K 136 LEU cc_start: 0.8517 (mp) cc_final: 0.8288 (mt) REVERT: K 175 GLU cc_start: 0.7091 (tt0) cc_final: 0.6886 (mt-10) REVERT: K 187 GLU cc_start: 0.6502 (mt-10) cc_final: 0.6224 (pt0) REVERT: K 192 GLN cc_start: 0.7673 (tp40) cc_final: 0.7414 (tm-30) outliers start: 34 outliers final: 4 residues processed: 316 average time/residue: 1.3349 time to fit residues: 448.8609 Evaluate side-chains 294 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 290 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain K residue 96 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 0.0870 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 50 GLN A 112 GLN A 193 ASN A 219 GLN C 112 GLN C 219 GLN E 112 GLN E 193 ASN G 21 ASN G 50 GLN G 193 ASN G 219 GLN I 21 ASN I 112 GLN I 219 GLN K 112 GLN K 193 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10566 Z= 0.366 Angle : 0.555 6.148 14364 Z= 0.279 Chirality : 0.045 0.163 1632 Planarity : 0.005 0.035 1854 Dihedral : 4.638 21.984 1410 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 4.53 % Allowed : 13.04 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.67 (0.22), residues: 1308 helix: 1.55 (0.17), residues: 894 sheet: -1.17 (0.54), residues: 54 loop : 0.59 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K 80 HIS 0.003 0.001 HIS K 84 PHE 0.012 0.002 PHE K 32 TYR 0.011 0.002 TYR E 145 ARG 0.002 0.000 ARG I 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 288 time to evaluate : 1.104 Fit side-chains REVERT: A 145 TYR cc_start: 0.8190 (m-80) cc_final: 0.7921 (m-10) REVERT: A 187 GLU cc_start: 0.6635 (mt-10) cc_final: 0.6336 (pt0) REVERT: A 197 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6652 (p0) REVERT: C 51 ASP cc_start: 0.8242 (m-30) cc_final: 0.7905 (m-30) REVERT: C 118 MET cc_start: 0.8739 (mtp) cc_final: 0.8408 (mtp) REVERT: C 197 ASP cc_start: 0.6889 (OUTLIER) cc_final: 0.6302 (p0) REVERT: E 51 ASP cc_start: 0.8246 (m-30) cc_final: 0.8024 (m-30) REVERT: E 136 LEU cc_start: 0.8578 (mp) cc_final: 0.8354 (mt) REVERT: E 175 GLU cc_start: 0.7426 (tt0) cc_final: 0.7169 (mt-10) REVERT: E 187 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6335 (pt0) REVERT: E 192 GLN cc_start: 0.7728 (tp40) cc_final: 0.7465 (tm-30) REVERT: E 197 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.6237 (p0) REVERT: G 145 TYR cc_start: 0.8190 (m-80) cc_final: 0.7920 (m-10) REVERT: G 187 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6336 (pt0) REVERT: G 197 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6657 (p0) REVERT: I 51 ASP cc_start: 0.8242 (m-30) cc_final: 0.7905 (m-30) REVERT: I 118 MET cc_start: 0.8739 (mtp) cc_final: 0.8407 (mtp) REVERT: I 197 ASP cc_start: 0.6892 (OUTLIER) cc_final: 0.6306 (p0) REVERT: K 51 ASP cc_start: 0.8245 (m-30) cc_final: 0.8023 (m-30) REVERT: K 136 LEU cc_start: 0.8579 (mp) cc_final: 0.8354 (mt) REVERT: K 175 GLU cc_start: 0.7428 (tt0) cc_final: 0.7172 (mt-10) REVERT: K 187 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6339 (pt0) REVERT: K 192 GLN cc_start: 0.7728 (tp40) cc_final: 0.7466 (tm-30) REVERT: K 197 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6235 (p0) outliers start: 50 outliers final: 22 residues processed: 294 average time/residue: 1.4219 time to fit residues: 444.2955 Evaluate side-chains 310 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 282 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 39 MET Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 197 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 80 optimal weight: 0.0870 chunk 120 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 114 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 50 GLN A 219 GLN C 112 GLN C 192 GLN C 219 GLN E 112 GLN G 21 ASN G 50 GLN G 219 GLN I 112 GLN I 192 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10566 Z= 0.183 Angle : 0.485 6.640 14364 Z= 0.237 Chirality : 0.041 0.167 1632 Planarity : 0.004 0.034 1854 Dihedral : 4.140 20.136 1410 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 4.17 % Allowed : 13.13 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.23), residues: 1308 helix: 1.94 (0.17), residues: 894 sheet: -0.65 (0.61), residues: 54 loop : 0.59 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 117 HIS 0.001 0.000 HIS C 84 PHE 0.011 0.002 PHE K 32 TYR 0.008 0.001 TYR K 145 ARG 0.005 0.000 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 300 time to evaluate : 1.238 Fit side-chains REVERT: A 145 TYR cc_start: 0.8137 (m-80) cc_final: 0.7892 (m-10) REVERT: A 187 GLU cc_start: 0.6620 (mt-10) cc_final: 0.6299 (pt0) REVERT: A 197 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6390 (p0) REVERT: C 18 ARG cc_start: 0.7492 (ttm-80) cc_final: 0.6838 (ttt-90) REVERT: C 51 ASP cc_start: 0.8167 (m-30) cc_final: 0.7804 (m-30) REVERT: C 68 MET cc_start: 0.8498 (mtm) cc_final: 0.8232 (mtm) REVERT: C 118 MET cc_start: 0.8768 (mtp) cc_final: 0.8504 (mtp) REVERT: C 197 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6240 (p0) REVERT: C 212 GLU cc_start: 0.7260 (tt0) cc_final: 0.6887 (tt0) REVERT: E 136 LEU cc_start: 0.8478 (mp) cc_final: 0.8251 (mt) REVERT: E 140 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8010 (mtpm) REVERT: E 179 GLN cc_start: 0.8536 (tp40) cc_final: 0.8303 (tp-100) REVERT: E 187 GLU cc_start: 0.6523 (mt-10) cc_final: 0.6232 (pt0) REVERT: E 192 GLN cc_start: 0.7671 (tp40) cc_final: 0.7420 (tm-30) REVERT: E 197 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6677 (p0) REVERT: G 145 TYR cc_start: 0.8141 (m-80) cc_final: 0.7894 (m-10) REVERT: G 187 GLU cc_start: 0.6620 (mt-10) cc_final: 0.6299 (pt0) REVERT: G 197 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6389 (p0) REVERT: I 51 ASP cc_start: 0.8169 (m-30) cc_final: 0.7807 (m-30) REVERT: I 68 MET cc_start: 0.8498 (mtm) cc_final: 0.8233 (mtm) REVERT: I 118 MET cc_start: 0.8768 (mtp) cc_final: 0.8503 (mtp) REVERT: I 197 ASP cc_start: 0.6840 (OUTLIER) cc_final: 0.6242 (p0) REVERT: I 212 GLU cc_start: 0.7260 (tt0) cc_final: 0.6889 (tt0) REVERT: K 136 LEU cc_start: 0.8477 (mp) cc_final: 0.8251 (mt) REVERT: K 140 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8013 (mtpm) REVERT: K 179 GLN cc_start: 0.8535 (tp40) cc_final: 0.8303 (tp-100) REVERT: K 187 GLU cc_start: 0.6519 (mt-10) cc_final: 0.6230 (pt0) REVERT: K 192 GLN cc_start: 0.7670 (tp40) cc_final: 0.7418 (tm-30) REVERT: K 197 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6678 (p0) outliers start: 46 outliers final: 18 residues processed: 306 average time/residue: 1.3966 time to fit residues: 453.9424 Evaluate side-chains 304 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 278 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 197 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN C 112 GLN C 179 GLN C 192 GLN C 219 GLN E 112 GLN E 219 GLN G 219 GLN I 112 GLN I 179 GLN I 192 GLN I 219 GLN K 112 GLN K 219 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10566 Z= 0.401 Angle : 0.568 6.643 14364 Z= 0.284 Chirality : 0.046 0.174 1632 Planarity : 0.005 0.037 1854 Dihedral : 4.580 22.351 1410 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 4.89 % Allowed : 14.67 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.68 (0.22), residues: 1308 helix: 1.54 (0.17), residues: 894 sheet: -0.91 (0.61), residues: 54 loop : 0.59 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 80 HIS 0.004 0.001 HIS E 12 PHE 0.014 0.002 PHE E 32 TYR 0.013 0.002 TYR K 145 ARG 0.006 0.000 ARG E 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 280 time to evaluate : 1.204 Fit side-chains REVERT: A 145 TYR cc_start: 0.8204 (m-80) cc_final: 0.7902 (m-10) REVERT: A 187 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6316 (pt0) REVERT: C 13 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: C 18 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6808 (ttt-90) REVERT: C 51 ASP cc_start: 0.8235 (m-30) cc_final: 0.7893 (m-30) REVERT: C 83 LEU cc_start: 0.7725 (mt) cc_final: 0.7434 (mt) REVERT: C 118 MET cc_start: 0.8695 (mtp) cc_final: 0.8376 (mtp) REVERT: C 197 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6389 (p0) REVERT: E 51 ASP cc_start: 0.8227 (m-30) cc_final: 0.7999 (m-30) REVERT: E 140 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8015 (mtpm) REVERT: E 187 GLU cc_start: 0.6587 (mt-10) cc_final: 0.6288 (pt0) REVERT: E 192 GLN cc_start: 0.7745 (tp40) cc_final: 0.7480 (tm-30) REVERT: E 197 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6657 (p0) REVERT: G 145 TYR cc_start: 0.8205 (m-80) cc_final: 0.7903 (m-10) REVERT: G 187 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6316 (pt0) REVERT: I 13 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: I 18 ARG cc_start: 0.7456 (mtm-85) cc_final: 0.6733 (ttt-90) REVERT: I 51 ASP cc_start: 0.8221 (m-30) cc_final: 0.7885 (m-30) REVERT: I 83 LEU cc_start: 0.7723 (mt) cc_final: 0.7434 (mt) REVERT: I 118 MET cc_start: 0.8669 (mtp) cc_final: 0.8359 (mtp) REVERT: I 197 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6390 (p0) REVERT: K 18 ARG cc_start: 0.7473 (ttm-80) cc_final: 0.6786 (ttt-90) REVERT: K 51 ASP cc_start: 0.8225 (m-30) cc_final: 0.7997 (m-30) REVERT: K 140 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8019 (mtpm) REVERT: K 187 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6290 (pt0) REVERT: K 192 GLN cc_start: 0.7749 (tp40) cc_final: 0.7484 (tm-30) REVERT: K 197 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6654 (p0) outliers start: 54 outliers final: 23 residues processed: 296 average time/residue: 1.4249 time to fit residues: 448.6425 Evaluate side-chains 301 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 269 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 197 ASP Chi-restraints excluded: chain K residue 203 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 106 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 219 GLN C 112 GLN C 219 GLN E 112 GLN G 50 GLN G 219 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10566 Z= 0.218 Angle : 0.497 6.896 14364 Z= 0.244 Chirality : 0.041 0.159 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.216 20.833 1410 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.99 % Allowed : 15.76 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.97 (0.23), residues: 1308 helix: 1.79 (0.17), residues: 894 sheet: -0.76 (0.68), residues: 54 loop : 0.60 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 117 HIS 0.002 0.001 HIS K 12 PHE 0.012 0.002 PHE E 32 TYR 0.010 0.001 TYR E 145 ARG 0.006 0.000 ARG E 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 275 time to evaluate : 1.179 Fit side-chains REVERT: A 145 TYR cc_start: 0.8162 (m-80) cc_final: 0.7897 (m-10) REVERT: A 187 GLU cc_start: 0.6609 (mt-10) cc_final: 0.6290 (pt0) REVERT: C 13 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: C 18 ARG cc_start: 0.7390 (ttm-80) cc_final: 0.6770 (ttt-90) REVERT: C 51 ASP cc_start: 0.8190 (m-30) cc_final: 0.7816 (m-30) REVERT: C 83 LEU cc_start: 0.7727 (mt) cc_final: 0.7481 (mt) REVERT: C 118 MET cc_start: 0.8726 (mtp) cc_final: 0.8472 (mtp) REVERT: C 197 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6345 (p0) REVERT: E 136 LEU cc_start: 0.8500 (mp) cc_final: 0.8290 (mt) REVERT: E 140 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8005 (mtpm) REVERT: E 179 GLN cc_start: 0.8556 (tp40) cc_final: 0.8282 (tp-100) REVERT: E 187 GLU cc_start: 0.6521 (mt-10) cc_final: 0.6289 (pt0) REVERT: E 192 GLN cc_start: 0.7702 (tp40) cc_final: 0.7459 (tm-30) REVERT: E 197 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6780 (p0) REVERT: G 145 TYR cc_start: 0.8164 (m-80) cc_final: 0.7897 (m-10) REVERT: G 187 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6291 (pt0) REVERT: I 13 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: I 18 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6788 (ttt-90) REVERT: I 51 ASP cc_start: 0.8185 (m-30) cc_final: 0.7817 (m-30) REVERT: I 83 LEU cc_start: 0.7728 (mt) cc_final: 0.7481 (mt) REVERT: I 118 MET cc_start: 0.8756 (mtp) cc_final: 0.8504 (mtp) REVERT: I 197 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6345 (p0) REVERT: K 18 ARG cc_start: 0.7490 (ttm-80) cc_final: 0.6795 (ttt-90) REVERT: K 140 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8012 (mtpm) REVERT: K 179 GLN cc_start: 0.8554 (tp40) cc_final: 0.8280 (tp-100) REVERT: K 187 GLU cc_start: 0.6520 (mt-10) cc_final: 0.6289 (pt0) REVERT: K 192 GLN cc_start: 0.7704 (tp40) cc_final: 0.7462 (tm-30) REVERT: K 197 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6782 (p0) outliers start: 44 outliers final: 21 residues processed: 289 average time/residue: 1.4207 time to fit residues: 436.0627 Evaluate side-chains 304 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 274 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 197 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 0.0770 chunk 78 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN C 112 GLN C 219 GLN E 112 GLN G 219 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10566 Z= 0.201 Angle : 0.499 7.326 14364 Z= 0.243 Chirality : 0.041 0.160 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.119 20.179 1410 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.80 % Allowed : 17.12 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.23), residues: 1308 helix: 1.87 (0.17), residues: 894 sheet: -0.69 (0.71), residues: 54 loop : 0.66 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 117 HIS 0.002 0.000 HIS A 12 PHE 0.011 0.002 PHE E 32 TYR 0.010 0.001 TYR K 145 ARG 0.007 0.000 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 284 time to evaluate : 1.248 Fit side-chains REVERT: A 145 TYR cc_start: 0.8162 (m-80) cc_final: 0.7862 (m-10) REVERT: A 185 MET cc_start: 0.8124 (mtm) cc_final: 0.7870 (mtt) REVERT: A 187 GLU cc_start: 0.6606 (mt-10) cc_final: 0.6288 (pt0) REVERT: C 13 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7464 (tt0) REVERT: C 18 ARG cc_start: 0.7440 (ttm-80) cc_final: 0.6839 (ttt-90) REVERT: C 51 ASP cc_start: 0.8157 (m-30) cc_final: 0.7777 (m-30) REVERT: C 83 LEU cc_start: 0.7792 (mt) cc_final: 0.7503 (mt) REVERT: C 118 MET cc_start: 0.8757 (mtp) cc_final: 0.8514 (mtp) REVERT: E 136 LEU cc_start: 0.8489 (mp) cc_final: 0.8269 (mt) REVERT: E 140 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7992 (mtpm) REVERT: E 179 GLN cc_start: 0.8489 (tp40) cc_final: 0.8281 (tp-100) REVERT: E 187 GLU cc_start: 0.6493 (mt-10) cc_final: 0.6239 (pt0) REVERT: E 192 GLN cc_start: 0.7699 (tp40) cc_final: 0.7460 (tm-30) REVERT: E 197 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6797 (p0) REVERT: G 145 TYR cc_start: 0.8163 (m-80) cc_final: 0.7860 (m-10) REVERT: G 185 MET cc_start: 0.8129 (mtm) cc_final: 0.7872 (mtt) REVERT: G 187 GLU cc_start: 0.6606 (mt-10) cc_final: 0.6285 (pt0) REVERT: I 13 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: I 18 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6803 (ttt-90) REVERT: I 51 ASP cc_start: 0.8152 (m-30) cc_final: 0.7775 (m-30) REVERT: I 83 LEU cc_start: 0.7791 (mt) cc_final: 0.7504 (mt) REVERT: I 118 MET cc_start: 0.8756 (mtp) cc_final: 0.8516 (mtp) REVERT: K 18 ARG cc_start: 0.7464 (ttm-80) cc_final: 0.6786 (ttt-90) REVERT: K 136 LEU cc_start: 0.8487 (mp) cc_final: 0.8263 (mt) REVERT: K 140 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8015 (mtpm) REVERT: K 179 GLN cc_start: 0.8488 (tp40) cc_final: 0.8280 (tp-100) REVERT: K 187 GLU cc_start: 0.6494 (mt-10) cc_final: 0.6241 (pt0) REVERT: K 192 GLN cc_start: 0.7699 (tp40) cc_final: 0.7461 (tm-30) REVERT: K 197 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6798 (p0) outliers start: 42 outliers final: 26 residues processed: 296 average time/residue: 1.4149 time to fit residues: 444.8624 Evaluate side-chains 309 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 276 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 197 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 GLN C 112 GLN C 219 GLN E 112 GLN G 112 GLN ** G 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10566 Z= 0.243 Angle : 0.508 7.122 14364 Z= 0.252 Chirality : 0.042 0.160 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.215 20.721 1410 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.99 % Allowed : 17.75 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.23), residues: 1308 helix: 1.83 (0.17), residues: 894 sheet: -0.61 (0.73), residues: 54 loop : 0.64 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 184 HIS 0.002 0.001 HIS A 12 PHE 0.012 0.002 PHE E 32 TYR 0.011 0.001 TYR K 145 ARG 0.007 0.000 ARG E 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 277 time to evaluate : 1.063 Fit side-chains REVERT: A 55 MET cc_start: 0.8164 (mtp) cc_final: 0.7815 (mtp) REVERT: A 145 TYR cc_start: 0.8159 (m-80) cc_final: 0.7885 (m-10) REVERT: A 185 MET cc_start: 0.8116 (mtm) cc_final: 0.7903 (mtt) REVERT: A 187 GLU cc_start: 0.6609 (mt-10) cc_final: 0.6304 (pt0) REVERT: A 197 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6636 (p0) REVERT: C 13 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7473 (tt0) REVERT: C 18 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.6774 (ttt-90) REVERT: C 51 ASP cc_start: 0.8165 (m-30) cc_final: 0.7786 (m-30) REVERT: C 83 LEU cc_start: 0.7725 (mt) cc_final: 0.7511 (mt) REVERT: C 118 MET cc_start: 0.8749 (mtp) cc_final: 0.8485 (mtp) REVERT: E 18 ARG cc_start: 0.7503 (ttm-80) cc_final: 0.6821 (ttt-90) REVERT: E 140 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8024 (mtpm) REVERT: E 179 GLN cc_start: 0.8506 (tp40) cc_final: 0.8260 (tp-100) REVERT: E 187 GLU cc_start: 0.6501 (mt-10) cc_final: 0.6268 (pt0) REVERT: E 192 GLN cc_start: 0.7705 (tp40) cc_final: 0.7464 (tm-30) REVERT: E 197 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6798 (p0) REVERT: G 55 MET cc_start: 0.8167 (mtp) cc_final: 0.7820 (mtp) REVERT: G 145 TYR cc_start: 0.8161 (m-80) cc_final: 0.7887 (m-10) REVERT: G 185 MET cc_start: 0.8116 (mtm) cc_final: 0.7903 (mtt) REVERT: G 187 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6305 (pt0) REVERT: G 197 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.6634 (p0) REVERT: I 13 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: I 18 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6778 (ttt-90) REVERT: I 51 ASP cc_start: 0.8163 (m-30) cc_final: 0.7786 (m-30) REVERT: I 83 LEU cc_start: 0.7725 (mt) cc_final: 0.7512 (mt) REVERT: I 118 MET cc_start: 0.8746 (mtp) cc_final: 0.8491 (mtp) REVERT: K 18 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.6821 (ttt-90) REVERT: K 140 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8031 (mtpm) REVERT: K 179 GLN cc_start: 0.8505 (tp40) cc_final: 0.8260 (tp-100) REVERT: K 187 GLU cc_start: 0.6503 (mt-10) cc_final: 0.6269 (pt0) REVERT: K 192 GLN cc_start: 0.7708 (tp40) cc_final: 0.7464 (tm-30) REVERT: K 197 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6800 (p0) outliers start: 44 outliers final: 31 residues processed: 289 average time/residue: 1.4488 time to fit residues: 443.8242 Evaluate side-chains 309 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 269 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 39 MET Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 197 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 107 optimal weight: 0.3980 chunk 112 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 125 optimal weight: 0.0980 chunk 76 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN C 219 GLN E 112 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10566 Z= 0.193 Angle : 0.500 7.497 14364 Z= 0.247 Chirality : 0.041 0.188 1632 Planarity : 0.004 0.034 1854 Dihedral : 4.069 19.962 1410 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.44 % Allowed : 19.29 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.23), residues: 1308 helix: 1.92 (0.18), residues: 894 sheet: -0.80 (0.73), residues: 54 loop : 0.62 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 117 HIS 0.002 0.000 HIS A 12 PHE 0.012 0.002 PHE E 32 TYR 0.010 0.001 TYR K 145 ARG 0.007 0.000 ARG E 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 284 time to evaluate : 1.283 Fit side-chains REVERT: A 145 TYR cc_start: 0.8164 (m-80) cc_final: 0.7860 (m-10) REVERT: A 187 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6188 (pt0) REVERT: A 197 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6547 (p0) REVERT: C 13 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: C 18 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.6761 (ttt-90) REVERT: C 51 ASP cc_start: 0.8153 (m-30) cc_final: 0.7775 (m-30) REVERT: C 118 MET cc_start: 0.8771 (mtp) cc_final: 0.8450 (mtp) REVERT: E 18 ARG cc_start: 0.7496 (ttm-80) cc_final: 0.6821 (ttt-90) REVERT: E 136 LEU cc_start: 0.8482 (mp) cc_final: 0.8259 (mt) REVERT: E 140 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8018 (mtpm) REVERT: E 187 GLU cc_start: 0.6494 (mt-10) cc_final: 0.6262 (pt0) REVERT: E 192 GLN cc_start: 0.7672 (tp40) cc_final: 0.7446 (tm-30) REVERT: E 197 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6781 (p0) REVERT: G 145 TYR cc_start: 0.8165 (m-80) cc_final: 0.7860 (m-10) REVERT: G 187 GLU cc_start: 0.6509 (mt-10) cc_final: 0.6186 (pt0) REVERT: G 197 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6548 (p0) REVERT: I 13 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: I 18 ARG cc_start: 0.7439 (mtm-85) cc_final: 0.6772 (ttt-90) REVERT: I 51 ASP cc_start: 0.8135 (m-30) cc_final: 0.7757 (m-30) REVERT: I 118 MET cc_start: 0.8762 (mtp) cc_final: 0.8445 (mtp) REVERT: K 18 ARG cc_start: 0.7438 (ttm-80) cc_final: 0.6790 (ttt-90) REVERT: K 136 LEU cc_start: 0.8481 (mp) cc_final: 0.8258 (mt) REVERT: K 140 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8023 (mtpm) REVERT: K 187 GLU cc_start: 0.6495 (mt-10) cc_final: 0.6263 (pt0) REVERT: K 192 GLN cc_start: 0.7673 (tp40) cc_final: 0.7444 (tm-30) REVERT: K 197 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6782 (p0) outliers start: 38 outliers final: 21 residues processed: 296 average time/residue: 1.4457 time to fit residues: 453.9567 Evaluate side-chains 306 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 277 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 197 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 121 optimal weight: 0.0770 chunk 104 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN C 219 GLN E 112 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10566 Z= 0.242 Angle : 0.522 7.648 14364 Z= 0.257 Chirality : 0.043 0.181 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.169 20.359 1410 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 3.44 % Allowed : 19.93 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.23), residues: 1308 helix: 1.82 (0.17), residues: 894 sheet: -0.72 (0.75), residues: 54 loop : 0.62 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 80 HIS 0.002 0.001 HIS A 12 PHE 0.012 0.002 PHE E 32 TYR 0.012 0.002 TYR E 145 ARG 0.007 0.000 ARG K 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 273 time to evaluate : 1.281 Fit side-chains REVERT: A 145 TYR cc_start: 0.8169 (m-80) cc_final: 0.7868 (m-10) REVERT: A 187 GLU cc_start: 0.6526 (mt-10) cc_final: 0.6214 (pt0) REVERT: A 197 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6621 (p0) REVERT: C 13 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: C 18 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.6748 (ttt-90) REVERT: C 51 ASP cc_start: 0.8163 (m-30) cc_final: 0.7782 (m-30) REVERT: C 83 LEU cc_start: 0.7783 (mt) cc_final: 0.7536 (mt) REVERT: C 118 MET cc_start: 0.8750 (mtp) cc_final: 0.8491 (mtp) REVERT: E 18 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.6824 (ttt-90) REVERT: E 136 LEU cc_start: 0.8502 (mp) cc_final: 0.8293 (mt) REVERT: E 140 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8022 (mtpm) REVERT: E 187 GLU cc_start: 0.6474 (mt-10) cc_final: 0.6197 (pt0) REVERT: E 192 GLN cc_start: 0.7685 (tp40) cc_final: 0.7450 (tm-30) REVERT: E 197 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6794 (p0) REVERT: G 55 MET cc_start: 0.8187 (mtp) cc_final: 0.7840 (mtp) REVERT: G 145 TYR cc_start: 0.8171 (m-80) cc_final: 0.7870 (m-10) REVERT: G 187 GLU cc_start: 0.6526 (mt-10) cc_final: 0.6216 (pt0) REVERT: G 197 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6618 (p0) REVERT: I 13 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: I 18 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6759 (ttt-90) REVERT: I 51 ASP cc_start: 0.8163 (m-30) cc_final: 0.7791 (m-30) REVERT: I 83 LEU cc_start: 0.7781 (mt) cc_final: 0.7536 (mt) REVERT: I 118 MET cc_start: 0.8775 (mtp) cc_final: 0.8515 (mtp) REVERT: K 18 ARG cc_start: 0.7439 (ttm-80) cc_final: 0.6795 (ttt-90) REVERT: K 136 LEU cc_start: 0.8504 (mp) cc_final: 0.8295 (mt) REVERT: K 140 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8027 (mtpm) REVERT: K 187 GLU cc_start: 0.6475 (mt-10) cc_final: 0.6198 (pt0) REVERT: K 192 GLN cc_start: 0.7686 (tp40) cc_final: 0.7449 (tm-30) REVERT: K 197 ASP cc_start: 0.7168 (OUTLIER) cc_final: 0.6794 (p0) outliers start: 38 outliers final: 19 residues processed: 283 average time/residue: 1.4899 time to fit residues: 446.6782 Evaluate side-chains 301 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 273 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 197 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 75 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: C 112 GLN C 219 GLN E 112 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.153373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115862 restraints weight = 10348.012| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.32 r_work: 0.3211 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10566 Z= 0.247 Angle : 0.524 7.795 14364 Z= 0.258 Chirality : 0.042 0.177 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.203 20.426 1410 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.90 % Allowed : 20.65 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.99 (0.23), residues: 1308 helix: 1.80 (0.17), residues: 894 sheet: -0.68 (0.76), residues: 54 loop : 0.61 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 80 HIS 0.002 0.001 HIS A 12 PHE 0.012 0.002 PHE K 32 TYR 0.012 0.002 TYR E 145 ARG 0.007 0.000 ARG K 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6245.78 seconds wall clock time: 110 minutes 47.86 seconds (6647.86 seconds total)