Starting phenix.real_space_refine on Thu Aug 6 16:06:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hqy_34954/08_2026/8hqy_34954.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hqy_34954/08_2026/8hqy_34954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hqy_34954/08_2026/8hqy_34954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hqy_34954/08_2026/8hqy_34954.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hqy_34954/08_2026/8hqy_34954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hqy_34954/08_2026/8hqy_34954.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5090 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 272 5.49 5 S 12 5.16 5 C 6888 2.51 5 N 2298 2.21 5 O 2832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12302 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 707 Classifications: {'peptide': 91} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 87} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 707 Classifications: {'peptide': 91} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 87} Chain: "S" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "U" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 593 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "I" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2775 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Chain: "J" Number of atoms: 2801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2801 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Time building chain proxies: 2.76, per 1000 atoms: 0.22 Number of scatterers: 12302 At special positions: 0 Unit cell: (123.51, 102.03, 115.992, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 272 15.00 O 2832 8.00 N 2298 7.00 C 6888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 379.0 milliseconds 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 11 sheets defined 67.0% alpha, 4.2% beta 135 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.984A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.667A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.665A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.605A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.718A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.534A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.683A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.676A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.533A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 4.124A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.070A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.722A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.494A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.710A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.678A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.567A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG H 99 " --> pdb=" O GLN H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.749A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 34 removed outlier: 3.529A pdb=" N LYS U 33 " --> pdb=" O LYS U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.783A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.569A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.528A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.786A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.495A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'U' and resid 12 through 16 removed outlier: 3.566A pdb=" N LEU U 15 " --> pdb=" O ILE U 3 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU U 69 " --> pdb=" O LYS U 6 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 343 hydrogen bonds 670 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 2020 1.32 - 1.44: 4361 1.44 - 1.56: 6123 1.56 - 1.68: 542 1.68 - 1.80: 23 Bond restraints: 13069 Sorted by residual: bond pdb=" C3' DG J 70 " pdb=" O3' DG J 70 " ideal model delta sigma weight residual 1.435 1.379 0.056 1.30e-02 5.92e+03 1.82e+01 bond pdb=" C3' DT I 68 " pdb=" O3' DT I 68 " ideal model delta sigma weight residual 1.435 1.381 0.054 1.30e-02 5.92e+03 1.73e+01 bond pdb=" C3' DG I 101 " pdb=" O3' DG I 101 " ideal model delta sigma weight residual 1.435 1.382 0.053 1.30e-02 5.92e+03 1.65e+01 bond pdb=" N1 DC J 93 " pdb=" C6 DC J 93 " ideal model delta sigma weight residual 1.367 1.343 0.024 6.00e-03 2.78e+04 1.65e+01 bond pdb=" C3' DG J 101 " pdb=" O3' DG J 101 " ideal model delta sigma weight residual 1.435 1.382 0.053 1.30e-02 5.92e+03 1.64e+01 ... (remaining 13064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 17878 2.39 - 4.78: 871 4.78 - 7.17: 50 7.17 - 9.56: 11 9.56 - 11.95: 3 Bond angle restraints: 18813 Sorted by residual: angle pdb=" O4' DT I 3 " pdb=" C4' DT I 3 " pdb=" C3' DT I 3 " ideal model delta sigma weight residual 106.00 102.53 3.47 6.00e-01 2.78e+00 3.35e+01 angle pdb=" O4' DC I 111 " pdb=" C4' DC I 111 " pdb=" C3' DC I 111 " ideal model delta sigma weight residual 106.00 102.78 3.22 6.00e-01 2.78e+00 2.88e+01 angle pdb=" O5' DG I 121 " pdb=" C5' DG I 121 " pdb=" C4' DG I 121 " ideal model delta sigma weight residual 109.40 113.57 -4.17 8.00e-01 1.56e+00 2.72e+01 angle pdb=" O4' DT J 143 " pdb=" C4' DT J 143 " pdb=" C3' DT J 143 " ideal model delta sigma weight residual 106.00 102.89 3.11 6.00e-01 2.78e+00 2.69e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.93 -3.03 6.00e-01 2.78e+00 2.54e+01 ... (remaining 18808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.96: 5473 28.96 - 57.93: 1574 57.93 - 86.89: 119 86.89 - 115.85: 1 115.85 - 144.82: 3 Dihedral angle restraints: 7170 sinusoidal: 4714 harmonic: 2456 Sorted by residual: dihedral pdb=" CA ALA A 114 " pdb=" C ALA A 114 " pdb=" N LYS A 115 " pdb=" CA LYS A 115 " ideal model delta harmonic sigma weight residual 180.00 156.65 23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA LEU U 71 " pdb=" C LEU U 71 " pdb=" N ARG U 72 " pdb=" CA ARG U 72 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA VAL U 70 " pdb=" C VAL U 70 " pdb=" N LEU U 71 " pdb=" CA LEU U 71 " ideal model delta harmonic sigma weight residual 180.00 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 7167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1464 0.061 - 0.122: 576 0.122 - 0.183: 92 0.183 - 0.244: 15 0.244 - 0.306: 2 Chirality restraints: 2149 Sorted by residual: chirality pdb=" CG LEU E 126 " pdb=" CB LEU E 126 " pdb=" CD1 LEU E 126 " pdb=" CD2 LEU E 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C3' DT I 68 " pdb=" C4' DT I 68 " pdb=" O3' DT I 68 " pdb=" C2' DT I 68 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C3' DG J 101 " pdb=" C4' DG J 101 " pdb=" O3' DG J 101 " pdb=" C2' DG J 101 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 2146 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " -0.021 2.00e-02 2.50e+03 1.82e-02 5.77e+00 pdb=" CG PHE G 25 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 25 " -0.018 2.00e-02 2.50e+03 1.75e-02 5.38e+00 pdb=" CG PHE C 25 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 25 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 25 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 25 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 25 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 25 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 113 " -0.015 2.00e-02 2.50e+03 1.74e-02 4.53e+00 pdb=" CG HIS A 113 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS A 113 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A 113 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 113 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS A 113 " -0.010 2.00e-02 2.50e+03 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2351 2.77 - 3.30: 10282 3.30 - 3.84: 24690 3.84 - 4.37: 28483 4.37 - 4.90: 40595 Nonbonded interactions: 106401 Sorted by model distance: nonbonded pdb=" O2 DC I 116 " pdb=" N2 DG J 32 " model vdw 2.238 2.496 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.264 3.040 nonbonded pdb=" N2 DG I 126 " pdb=" O2 DC J 22 " model vdw 2.274 2.496 nonbonded pdb=" O HIS D 109 " pdb=" OG SER D 112 " model vdw 2.288 3.040 nonbonded pdb=" OE1 GLN A 68 " pdb=" NH1 ARG A 72 " model vdw 2.291 3.120 ... (remaining 106396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 13 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.730 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.113 13069 Z= 0.886 Angle : 1.121 11.952 18813 Z= 0.865 Chirality : 0.063 0.306 2149 Planarity : 0.007 0.052 1438 Dihedral : 27.346 144.817 5584 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.14 % Allowed : 3.24 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.24), residues: 828 helix: -1.68 (0.18), residues: 551 sheet: -3.05 (0.99), residues: 20 loop : -2.24 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 116 TYR 0.021 0.003 TYR F 98 PHE 0.040 0.005 PHE C 25 TRP 0.005 0.002 TRP S 164 HIS 0.020 0.004 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.01175 / 0.89 (13069) covalent geometry : angle 1.12051 / 0.86 (18813) hydrogen bonds : bond 0.11152 / 7.20 ( 746) hydrogen bonds : angle 4.17515 / 2.88 ( 1855) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 306 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9107 (tptt) cc_final: 0.8691 (tptp) REVERT: B 88 TYR cc_start: 0.8837 (m-10) cc_final: 0.8137 (m-10) REVERT: C 32 ARG cc_start: 0.8854 (ttp80) cc_final: 0.8445 (tmm-80) REVERT: C 104 GLN cc_start: 0.8399 (mm110) cc_final: 0.8064 (mm-40) REVERT: D 105 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7819 (tp30) REVERT: E 41 TYR cc_start: 0.8368 (m-80) cc_final: 0.8006 (m-10) REVERT: F 59 LYS cc_start: 0.9203 (tptm) cc_final: 0.8663 (mmmm) REVERT: F 88 TYR cc_start: 0.8962 (m-10) cc_final: 0.8478 (m-80) REVERT: G 112 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8856 (mm110) REVERT: H 59 MET cc_start: 0.8941 (tpp) cc_final: 0.8615 (tpp) REVERT: H 83 TYR cc_start: 0.8318 (m-10) cc_final: 0.7988 (m-10) REVERT: U 48 LYS cc_start: 0.8553 (pttt) cc_final: 0.8178 (pttp) REVERT: U 50 LEU cc_start: 0.7793 (mm) cc_final: 0.7516 (mm) REVERT: U 63 LYS cc_start: 0.7992 (mttt) cc_final: 0.7710 (mtpp) REVERT: U 68 HIS cc_start: 0.8526 (m-70) cc_final: 0.8247 (m90) outliers start: 1 outliers final: 1 residues processed: 307 average time/residue: 0.1568 time to fit residues: 62.9274 Evaluate side-chains 218 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 40.0000 chunk 38 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN D 47 GLN D 63 ASN E 76 GLN E 93 GLN F 75 HIS G 104 GLN ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 49 GLN U 68 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.060277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.038685 restraints weight = 54036.978| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.47 r_work: 0.2605 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13069 Z= 0.159 Angle : 0.764 14.432 18813 Z= 0.432 Chirality : 0.053 0.274 2149 Planarity : 0.005 0.052 1438 Dihedral : 31.560 149.447 3909 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.39 % Allowed : 10.86 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.28), residues: 828 helix: 0.14 (0.21), residues: 555 sheet: -2.25 (1.05), residues: 20 loop : -1.94 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 23 TYR 0.027 0.002 TYR D 83 PHE 0.014 0.002 PHE A 67 TRP 0.005 0.002 TRP S 164 HIS 0.005 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (13069) covalent geometry : angle 0.76351 / 0.43 (18813) hydrogen bonds : bond 0.06634 / 4.50 ( 746) hydrogen bonds : angle 3.39149 / 2.33 ( 1855) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 255 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8983 (mt-10) REVERT: A 68 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.9085 (tm-30) REVERT: A 73 GLU cc_start: 0.9045 (tt0) cc_final: 0.8746 (tt0) REVERT: A 106 ASP cc_start: 0.8761 (m-30) cc_final: 0.8377 (m-30) REVERT: B 44 LYS cc_start: 0.9417 (ttpp) cc_final: 0.9172 (mtpt) REVERT: C 38 ASN cc_start: 0.8911 (m-40) cc_final: 0.8702 (m-40) REVERT: C 92 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7991 (mt-10) REVERT: E 93 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8578 (tp40) REVERT: F 25 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8497 (m-40) REVERT: G 38 ASN cc_start: 0.9037 (m-40) cc_final: 0.8806 (m-40) REVERT: G 56 GLU cc_start: 0.8896 (tt0) cc_final: 0.8557 (mt-10) REVERT: G 92 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8449 (mt-10) REVERT: G 112 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8612 (mm110) REVERT: H 59 MET cc_start: 0.9291 (tpp) cc_final: 0.8934 (tpp) REVERT: H 71 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8635 (tp30) REVERT: H 83 TYR cc_start: 0.8481 (m-10) cc_final: 0.8132 (m-10) REVERT: U 15 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8326 (pp) REVERT: U 48 LYS cc_start: 0.8584 (pttt) cc_final: 0.8222 (pttp) REVERT: U 63 LYS cc_start: 0.7893 (mttt) cc_final: 0.7574 (mtpp) outliers start: 24 outliers final: 15 residues processed: 267 average time/residue: 0.1219 time to fit residues: 45.6618 Evaluate side-chains 254 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 11 LYS Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 79 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 93 optimal weight: 30.0000 chunk 84 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 63 ASN E 93 GLN G 73 ASN G 104 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.059290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.038211 restraints weight = 53772.443| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.47 r_work: 0.2564 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13069 Z= 0.234 Angle : 0.754 7.613 18813 Z= 0.426 Chirality : 0.052 0.254 2149 Planarity : 0.005 0.035 1438 Dihedral : 31.326 148.219 3909 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.09 % Allowed : 13.96 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.29), residues: 828 helix: 0.94 (0.22), residues: 553 sheet: -2.18 (0.93), residues: 20 loop : -1.77 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG U 42 TYR 0.023 0.002 TYR D 83 PHE 0.013 0.002 PHE E 67 TRP 0.007 0.003 TRP S 164 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.23 (13069) covalent geometry : angle 0.75381 / 0.43 (18813) hydrogen bonds : bond 0.06676 / 4.46 ( 746) hydrogen bonds : angle 3.33971 / 2.29 ( 1855) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9347 (mt-10) cc_final: 0.9009 (mt-10) REVERT: A 94 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8748 (mt-10) REVERT: A 106 ASP cc_start: 0.8791 (m-30) cc_final: 0.8388 (m-30) REVERT: B 44 LYS cc_start: 0.9484 (ttpp) cc_final: 0.9250 (mtpt) REVERT: C 92 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8271 (mt-10) REVERT: C 94 ASN cc_start: 0.9377 (OUTLIER) cc_final: 0.9130 (t0) REVERT: E 79 LYS cc_start: 0.8966 (tptp) cc_final: 0.8742 (tptp) REVERT: F 25 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8534 (m-40) REVERT: G 38 ASN cc_start: 0.9087 (m-40) cc_final: 0.8816 (m-40) REVERT: G 92 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8512 (mt-10) REVERT: G 112 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8600 (mm110) REVERT: H 59 MET cc_start: 0.9301 (tpp) cc_final: 0.8998 (tpp) REVERT: H 83 TYR cc_start: 0.8571 (m-10) cc_final: 0.8360 (m-80) REVERT: H 93 GLU cc_start: 0.8840 (mp0) cc_final: 0.8548 (mp0) REVERT: U 48 LYS cc_start: 0.8561 (pttt) cc_final: 0.8245 (pttp) REVERT: U 63 LYS cc_start: 0.7820 (mttt) cc_final: 0.7481 (mtpp) outliers start: 29 outliers final: 15 residues processed: 244 average time/residue: 0.1229 time to fit residues: 42.1034 Evaluate side-chains 240 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 43 LEU Chi-restraints excluded: chain U residue 58 ASP Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 29 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 47 GLN H 84 ASN ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.060029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.038498 restraints weight = 53728.678| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.49 r_work: 0.2589 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13069 Z= 0.153 Angle : 0.690 7.712 18813 Z= 0.399 Chirality : 0.049 0.270 2149 Planarity : 0.004 0.033 1438 Dihedral : 31.141 149.204 3908 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.10 % Allowed : 16.36 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.30), residues: 828 helix: 1.41 (0.22), residues: 553 sheet: -1.98 (1.02), residues: 19 loop : -1.74 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 128 TYR 0.019 0.001 TYR C 57 PHE 0.013 0.001 PHE D 65 TRP 0.006 0.002 TRP S 164 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (13069) covalent geometry : angle 0.69018 / 0.40 (18813) hydrogen bonds : bond 0.05889 / 3.98 ( 746) hydrogen bonds : angle 3.14167 / 2.15 ( 1855) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 236 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9342 (mt-10) cc_final: 0.8973 (mt-10) REVERT: A 62 ILE cc_start: 0.9450 (mp) cc_final: 0.8411 (mp) REVERT: A 68 GLN cc_start: 0.9321 (tm-30) cc_final: 0.8695 (tm-30) REVERT: A 94 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8763 (mt-10) REVERT: C 64 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8847 (tm-30) REVERT: E 79 LYS cc_start: 0.8862 (tptp) cc_final: 0.8561 (tptp) REVERT: E 93 GLN cc_start: 0.8842 (tt0) cc_final: 0.8551 (tp40) REVERT: E 120 MET cc_start: 0.8966 (mmm) cc_final: 0.8710 (mmm) REVERT: F 25 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8546 (m-40) REVERT: G 56 GLU cc_start: 0.8942 (tt0) cc_final: 0.8719 (mt-10) REVERT: G 89 ASN cc_start: 0.9151 (m110) cc_final: 0.8539 (m110) REVERT: G 92 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8498 (mt-10) REVERT: G 112 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8601 (mm110) REVERT: H 59 MET cc_start: 0.9316 (tpp) cc_final: 0.9043 (tpp) REVERT: H 71 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8685 (tp30) REVERT: H 93 GLU cc_start: 0.8807 (mp0) cc_final: 0.8539 (mp0) REVERT: U 29 LYS cc_start: 0.8985 (mmmm) cc_final: 0.8689 (mptt) REVERT: U 48 LYS cc_start: 0.8457 (pttt) cc_final: 0.8146 (pttp) REVERT: U 63 LYS cc_start: 0.7734 (mttt) cc_final: 0.7441 (mtpp) outliers start: 22 outliers final: 10 residues processed: 244 average time/residue: 0.1272 time to fit residues: 43.2998 Evaluate side-chains 243 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 232 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain U residue 43 LEU Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 81 optimal weight: 50.0000 chunk 59 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.059566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.038336 restraints weight = 54300.140| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.45 r_work: 0.2585 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13069 Z= 0.179 Angle : 0.692 7.238 18813 Z= 0.396 Chirality : 0.049 0.263 2149 Planarity : 0.004 0.034 1438 Dihedral : 31.042 149.515 3908 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.53 % Allowed : 17.35 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.30), residues: 828 helix: 1.72 (0.22), residues: 553 sheet: -1.97 (1.03), residues: 19 loop : -1.69 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 29 TYR 0.019 0.002 TYR C 57 PHE 0.013 0.001 PHE D 65 TRP 0.007 0.003 TRP S 164 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 (13069) covalent geometry : angle 0.69211 / 0.40 (18813) hydrogen bonds : bond 0.05910 / 3.97 ( 746) hydrogen bonds : angle 3.12872 / 2.15 ( 1855) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8974 (mt-10) REVERT: A 68 GLN cc_start: 0.9291 (tm-30) cc_final: 0.8676 (tm-30) REVERT: A 94 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8758 (mt-10) REVERT: A 97 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8770 (mm-30) REVERT: B 44 LYS cc_start: 0.9350 (mtpt) cc_final: 0.9083 (mtpp) REVERT: C 64 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8825 (tm-30) REVERT: D 68 ASP cc_start: 0.9321 (t70) cc_final: 0.8913 (t0) REVERT: E 79 LYS cc_start: 0.8871 (tptp) cc_final: 0.8508 (tptp) REVERT: E 93 GLN cc_start: 0.8898 (tt0) cc_final: 0.8572 (tp40) REVERT: E 120 MET cc_start: 0.9037 (mmm) cc_final: 0.8798 (mmm) REVERT: F 25 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8510 (m-40) REVERT: G 56 GLU cc_start: 0.8943 (tt0) cc_final: 0.8597 (mt-10) REVERT: G 89 ASN cc_start: 0.9143 (m110) cc_final: 0.8548 (m110) REVERT: G 112 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8605 (mm110) REVERT: H 59 MET cc_start: 0.9330 (tpp) cc_final: 0.9072 (tpp) REVERT: H 83 TYR cc_start: 0.8562 (m-10) cc_final: 0.8288 (m-10) REVERT: H 93 GLU cc_start: 0.8819 (mp0) cc_final: 0.8503 (mp0) REVERT: U 24 GLU cc_start: 0.9202 (pm20) cc_final: 0.8975 (pm20) REVERT: U 29 LYS cc_start: 0.8976 (mmmm) cc_final: 0.8685 (mptt) REVERT: U 63 LYS cc_start: 0.7691 (mttt) cc_final: 0.7440 (mtpp) REVERT: U 73 LEU cc_start: 0.7726 (tp) cc_final: 0.7274 (tp) outliers start: 25 outliers final: 16 residues processed: 241 average time/residue: 0.1257 time to fit residues: 42.2230 Evaluate side-chains 241 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 224 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain U residue 43 LEU Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 5 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 53 optimal weight: 0.0040 chunk 45 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.060276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.039138 restraints weight = 54315.051| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.43 r_work: 0.2612 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13069 Z= 0.141 Angle : 0.662 6.779 18813 Z= 0.386 Chirality : 0.047 0.271 2149 Planarity : 0.004 0.034 1438 Dihedral : 30.901 149.554 3908 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.53 % Allowed : 19.18 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.30), residues: 828 helix: 1.97 (0.22), residues: 551 sheet: -1.85 (1.02), residues: 19 loop : -1.63 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 72 TYR 0.019 0.001 TYR C 57 PHE 0.016 0.001 PHE D 65 TRP 0.004 0.002 TRP S 164 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (13069) covalent geometry : angle 0.66235 / 0.39 (18813) hydrogen bonds : bond 0.05641 / 3.82 ( 746) hydrogen bonds : angle 3.01157 / 2.06 ( 1855) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8976 (mt-10) REVERT: A 68 GLN cc_start: 0.9268 (tm-30) cc_final: 0.8694 (tm-30) REVERT: A 94 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8745 (mt-10) REVERT: B 44 LYS cc_start: 0.9330 (mtpt) cc_final: 0.9063 (mtpp) REVERT: C 64 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8931 (tm-30) REVERT: D 68 ASP cc_start: 0.9277 (t70) cc_final: 0.8949 (t0) REVERT: E 79 LYS cc_start: 0.8884 (tptp) cc_final: 0.8515 (tptp) REVERT: E 120 MET cc_start: 0.8978 (mmm) cc_final: 0.8744 (mmm) REVERT: F 25 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8509 (m-40) REVERT: G 56 GLU cc_start: 0.8937 (tt0) cc_final: 0.8731 (mt-10) REVERT: G 89 ASN cc_start: 0.9154 (m110) cc_final: 0.8582 (m110) REVERT: G 92 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8521 (mt-10) REVERT: G 112 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8582 (mm110) REVERT: H 59 MET cc_start: 0.9332 (tpp) cc_final: 0.9116 (tpp) REVERT: H 83 TYR cc_start: 0.8516 (m-10) cc_final: 0.8286 (m-80) REVERT: H 93 GLU cc_start: 0.8793 (mp0) cc_final: 0.8481 (mp0) REVERT: H 105 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8212 (tp30) REVERT: U 29 LYS cc_start: 0.8970 (mmmm) cc_final: 0.8703 (mptt) REVERT: U 63 LYS cc_start: 0.7669 (mttt) cc_final: 0.7446 (mtpp) outliers start: 25 outliers final: 17 residues processed: 250 average time/residue: 0.1233 time to fit residues: 43.1621 Evaluate side-chains 249 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain U residue 43 LEU Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 78 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 50.0000 chunk 91 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.060232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.038786 restraints weight = 53579.507| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.44 r_work: 0.2608 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13069 Z= 0.150 Angle : 0.669 7.257 18813 Z= 0.385 Chirality : 0.047 0.266 2149 Planarity : 0.004 0.035 1438 Dihedral : 30.833 149.336 3908 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.81 % Allowed : 20.31 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.30), residues: 828 helix: 2.06 (0.22), residues: 553 sheet: -1.87 (1.00), residues: 19 loop : -1.56 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.022 0.001 TYR C 57 PHE 0.016 0.001 PHE D 65 TRP 0.005 0.002 TRP S 164 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (13069) covalent geometry : angle 0.66868 / 0.39 (18813) hydrogen bonds : bond 0.05581 / 3.76 ( 746) hydrogen bonds : angle 3.01456 / 2.07 ( 1855) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9330 (mt-10) cc_final: 0.8987 (mt-10) REVERT: A 68 GLN cc_start: 0.9262 (tm-30) cc_final: 0.8841 (tm-30) REVERT: A 94 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8736 (mt-10) REVERT: B 44 LYS cc_start: 0.9344 (mtpt) cc_final: 0.9071 (mtpp) REVERT: C 64 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8933 (tm-30) REVERT: C 92 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8257 (mt-10) REVERT: D 46 LYS cc_start: 0.9343 (mmmt) cc_final: 0.9099 (mmmt) REVERT: D 68 ASP cc_start: 0.9300 (t70) cc_final: 0.8947 (t0) REVERT: F 25 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8184 (m-40) REVERT: F 62 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9115 (mp) REVERT: G 38 ASN cc_start: 0.8983 (m-40) cc_final: 0.8772 (m-40) REVERT: G 56 GLU cc_start: 0.8955 (tt0) cc_final: 0.8752 (mt-10) REVERT: G 89 ASN cc_start: 0.9141 (m110) cc_final: 0.8582 (m110) REVERT: G 92 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8543 (mt-10) REVERT: H 93 GLU cc_start: 0.8808 (mp0) cc_final: 0.8476 (mp0) REVERT: H 105 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8183 (tp30) REVERT: U 63 LYS cc_start: 0.7688 (mttt) cc_final: 0.7471 (mtpp) outliers start: 27 outliers final: 18 residues processed: 239 average time/residue: 0.1232 time to fit residues: 41.0473 Evaluate side-chains 245 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 43 LEU Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 74 optimal weight: 0.2980 chunk 58 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 81 optimal weight: 50.0000 chunk 69 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.060303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.039515 restraints weight = 53291.070| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.39 r_work: 0.2617 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13069 Z= 0.152 Angle : 0.675 7.061 18813 Z= 0.387 Chirality : 0.046 0.267 2149 Planarity : 0.004 0.034 1438 Dihedral : 30.795 149.149 3908 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.24 % Allowed : 20.87 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.31), residues: 828 helix: 2.13 (0.22), residues: 551 sheet: -1.92 (1.03), residues: 19 loop : -1.48 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 29 TYR 0.026 0.001 TYR C 57 PHE 0.016 0.001 PHE D 65 TRP 0.005 0.002 TRP S 164 HIS 0.006 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (13069) covalent geometry : angle 0.67466 / 0.39 (18813) hydrogen bonds : bond 0.05510 / 3.70 ( 746) hydrogen bonds : angle 2.99854 / 2.06 ( 1855) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9309 (mt-10) cc_final: 0.8963 (mt-10) REVERT: A 68 GLN cc_start: 0.9231 (tm-30) cc_final: 0.8840 (tm-30) REVERT: A 94 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8706 (mt-10) REVERT: B 44 LYS cc_start: 0.9357 (mtpt) cc_final: 0.9079 (mtpp) REVERT: C 64 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8918 (tm-30) REVERT: C 89 ASN cc_start: 0.9417 (m-40) cc_final: 0.9004 (m110) REVERT: D 46 LYS cc_start: 0.9356 (mmmt) cc_final: 0.9155 (mmmt) REVERT: D 68 ASP cc_start: 0.9292 (t70) cc_final: 0.8916 (t0) REVERT: E 79 LYS cc_start: 0.8817 (tptp) cc_final: 0.8540 (tptp) REVERT: F 25 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8488 (m-40) REVERT: F 88 TYR cc_start: 0.9081 (m-10) cc_final: 0.8566 (m-10) REVERT: G 38 ASN cc_start: 0.8970 (m-40) cc_final: 0.8753 (m-40) REVERT: G 56 GLU cc_start: 0.8944 (tt0) cc_final: 0.8742 (mt-10) REVERT: G 89 ASN cc_start: 0.9126 (m110) cc_final: 0.8554 (m110) REVERT: H 83 TYR cc_start: 0.8259 (m-10) cc_final: 0.8028 (m-80) REVERT: H 93 GLU cc_start: 0.8813 (mp0) cc_final: 0.8511 (mp0) REVERT: H 105 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8140 (tp30) outliers start: 23 outliers final: 15 residues processed: 243 average time/residue: 0.1273 time to fit residues: 43.1555 Evaluate side-chains 243 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 227 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 44 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.060012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.038721 restraints weight = 53719.743| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.42 r_work: 0.2594 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13069 Z= 0.174 Angle : 0.687 9.325 18813 Z= 0.391 Chirality : 0.047 0.265 2149 Planarity : 0.004 0.034 1438 Dihedral : 30.797 148.836 3908 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.24 % Allowed : 21.30 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.31), residues: 828 helix: 2.12 (0.22), residues: 555 sheet: -2.23 (0.97), residues: 19 loop : -1.43 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 128 TYR 0.022 0.002 TYR C 57 PHE 0.016 0.001 PHE D 65 TRP 0.005 0.002 TRP S 164 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (13069) covalent geometry : angle 0.68743 / 0.39 (18813) hydrogen bonds : bond 0.05560 / 3.73 ( 746) hydrogen bonds : angle 3.05788 / 2.10 ( 1855) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9330 (mt-10) cc_final: 0.8973 (mt-10) REVERT: B 44 LYS cc_start: 0.9365 (mtpt) cc_final: 0.9091 (mtpp) REVERT: C 64 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8941 (tm-30) REVERT: C 118 LYS cc_start: 0.7984 (mmmt) cc_final: 0.7264 (mmmt) REVERT: D 46 LYS cc_start: 0.9388 (mmmt) cc_final: 0.9151 (mmmt) REVERT: D 68 ASP cc_start: 0.9307 (t70) cc_final: 0.8923 (t0) REVERT: F 25 ASN cc_start: 0.9027 (OUTLIER) cc_final: 0.8175 (m-40) REVERT: F 88 TYR cc_start: 0.9175 (m-10) cc_final: 0.8487 (m-10) REVERT: G 38 ASN cc_start: 0.8962 (m-40) cc_final: 0.8753 (m-40) REVERT: G 56 GLU cc_start: 0.8958 (tt0) cc_final: 0.8746 (mt-10) REVERT: G 89 ASN cc_start: 0.9155 (m110) cc_final: 0.8579 (m110) REVERT: G 92 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8529 (mt-10) REVERT: H 83 TYR cc_start: 0.8414 (m-10) cc_final: 0.8150 (m-80) REVERT: H 93 GLU cc_start: 0.8839 (mp0) cc_final: 0.8467 (mp0) REVERT: S 175 VAL cc_start: 0.9026 (t) cc_final: 0.8642 (p) REVERT: U 6 LYS cc_start: 0.8889 (ttmt) cc_final: 0.8020 (mttm) REVERT: U 39 ASP cc_start: 0.8680 (p0) cc_final: 0.7977 (p0) outliers start: 23 outliers final: 19 residues processed: 234 average time/residue: 0.1353 time to fit residues: 43.8256 Evaluate side-chains 242 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain U residue 43 LEU Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 30 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 94 optimal weight: 50.0000 chunk 102 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.059746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.038985 restraints weight = 54046.533| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.35 r_work: 0.2593 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13069 Z= 0.192 Angle : 0.719 9.082 18813 Z= 0.402 Chirality : 0.047 0.265 2149 Planarity : 0.004 0.034 1438 Dihedral : 30.824 148.534 3908 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.10 % Allowed : 21.58 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.30), residues: 828 helix: 2.09 (0.22), residues: 555 sheet: -2.38 (0.98), residues: 19 loop : -1.36 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG U 74 TYR 0.027 0.002 TYR C 57 PHE 0.016 0.002 PHE D 65 TRP 0.005 0.002 TRP S 164 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (13069) covalent geometry : angle 0.71852 / 0.40 (18813) hydrogen bonds : bond 0.05639 / 3.78 ( 746) hydrogen bonds : angle 3.09495 / 2.13 ( 1855) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1656 Ramachandran restraints generated. 828 Oldfield, 0 Emsley, 828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8976 (mt-10) REVERT: A 94 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8755 (mt-10) REVERT: B 44 LYS cc_start: 0.9391 (mtpt) cc_final: 0.9119 (mtpp) REVERT: C 64 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8944 (tm-30) REVERT: C 118 LYS cc_start: 0.7903 (mmmt) cc_final: 0.7296 (mmmt) REVERT: D 68 ASP cc_start: 0.9286 (t70) cc_final: 0.8895 (t0) REVERT: F 25 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8500 (m-40) REVERT: F 88 TYR cc_start: 0.9218 (m-10) cc_final: 0.8524 (m-10) REVERT: G 38 ASN cc_start: 0.8966 (m-40) cc_final: 0.8758 (m-40) REVERT: G 56 GLU cc_start: 0.8986 (tt0) cc_final: 0.8640 (mt-10) REVERT: G 89 ASN cc_start: 0.9146 (m110) cc_final: 0.8554 (m110) REVERT: G 92 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8518 (mt-10) REVERT: H 71 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8750 (tp30) REVERT: H 83 TYR cc_start: 0.8388 (m-10) cc_final: 0.8128 (m-80) REVERT: H 93 GLU cc_start: 0.8850 (mp0) cc_final: 0.8494 (mp0) REVERT: S 175 VAL cc_start: 0.9070 (t) cc_final: 0.8743 (p) REVERT: U 39 ASP cc_start: 0.8672 (p0) cc_final: 0.7941 (p0) outliers start: 22 outliers final: 19 residues processed: 234 average time/residue: 0.1354 time to fit residues: 43.6893 Evaluate side-chains 240 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain U residue 25 ASN Chi-restraints excluded: chain U residue 43 LEU Chi-restraints excluded: chain U residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 6 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 62 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.060536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.039441 restraints weight = 53656.200| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.40 r_work: 0.2622 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13069 Z= 0.141 Angle : 0.691 9.211 18813 Z= 0.391 Chirality : 0.046 0.273 2149 Planarity : 0.004 0.034 1438 Dihedral : 30.731 147.777 3908 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.83 % Allowed : 22.71 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.31), residues: 828 helix: 2.16 (0.22), residues: 555 sheet: -2.28 (1.03), residues: 19 loop : -1.24 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.025 0.001 TYR C 57 PHE 0.018 0.001 PHE D 65 TRP 0.006 0.002 TRP S 164 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (13069) covalent geometry : angle 0.69058 / 0.39 (18813) hydrogen bonds : bond 0.05412 / 3.65 ( 746) hydrogen bonds : angle 2.99985 / 2.06 ( 1855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3480.59 seconds wall clock time: 60 minutes 5.71 seconds (3605.71 seconds total)