Starting phenix.real_space_refine on Fri Jul 3 20:35:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hqy_34954/07_2026/8hqy_34954.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hqy_34954/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hqy_34954/07_2026/8hqy_34954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hqy_34954/07_2026/8hqy_34954.map" model { file = "/net/cci-nas-00/data/ceres_data/8hqy_34954/07_2026/8hqy_34954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hqy_34954/07_2026/8hqy_34954.cif" } 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-dev-6108/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: 2.94, per 1000 atoms: 0.24 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: 1.03 Conformation dependent library (CDL) restraints added in 519.0 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: 1.87 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: 2.27 Time building geometry restraints manager: 1.38 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: 17885 2.39 - 4.78: 864 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: 1.230 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.230 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 17.220 ------------------------------------------------------------------------------- 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= 0.885 Angle : 1.115 11.952 18813 Z= 0.859 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 1.11486 / 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 : 0.411 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: 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: 0.8138 (m-10) 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: 0.8007 (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 15 LYS cc_start: 0.8776 (ttmm) cc_final: 0.8382 (tmmt) 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: 0.8616 (tpp) REVERT: H 83 TYR cc_start: 0.8318 (m-10) cc_final: 0.7991 (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: 0.1678 time to fit residues: 66.9517 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 : 0.348 ------------------------------------------------------------------------------- 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: 10.0000 chunk 53 optimal weight: 0.9980 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: 30.0000 chunk 38 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.060262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.039075 restraints weight = 53740.258| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.44 r_work: 0.2608 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 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 = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13069 Z= 0.164 Angle : 0.752 13.946 18813 Z= 0.429 Chirality : 0.052 0.258 2149 Planarity : 0.005 0.051 1438 Dihedral : 31.625 149.968 3909 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.10 % Allowed : 10.44 % Favored : 86.46 % 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: -0.91 (0.28), residues: 828 helix: 0.11 (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 0.007 0.001 ARG B 23 TYR 0.027 0.002 TYR D 83 PHE 0.013 0.002 PHE A 67 TRP 0.005 0.002 TRP S 164 HIS 0.006 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 (13069) covalent geometry : angle 0.75196 / 0.43 (18813) hydrogen bonds : bond 0.06636 / 4.50 ( 746) hydrogen bonds : angle 3.39951 / 2.34 ( 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 278 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 256 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8983 (mt-10) REVERT: A 68 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.9097 (tm-30) REVERT: A 73 GLU cc_start: 0.9036 (tt0) cc_final: 0.8741 (tt0) REVERT: A 106 ASP cc_start: 0.8751 (m-30) cc_final: 0.8365 (m-30) REVERT: B 44 LYS cc_start: 0.9412 (ttpp) cc_final: 0.9167 (mtpt) REVERT: B 84 MET cc_start: 0.8656 (tpp) cc_final: 0.8450 (tpp) REVERT: C 38 ASN cc_start: 0.8912 (m-40) cc_final: 0.8700 (m-40) REVERT: C 92 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7987 (mt-10) REVERT: E 93 GLN cc_start: 0.8970 (tp-100) cc_final: 0.8573 (tp40) REVERT: F 25 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8493 (m-40) REVERT: G 15 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8221 (tmmt) REVERT: G 38 ASN cc_start: 0.9034 (m-40) cc_final: 0.8802 (m-40) REVERT: G 56 GLU cc_start: 0.8893 (tt0) cc_final: 0.8546 (mt-10) REVERT: G 92 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8457 (mt-10) REVERT: G 112 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8622 (mm110) REVERT: H 59 MET cc_start: 0.9290 (tpp) cc_final: 0.8931 (tpp) REVERT: H 71 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8641 (tp30) REVERT: H 83 TYR cc_start: 0.8484 (m-10) cc_final: 0.8135 (m-10) REVERT: U 15 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8308 (pp) REVERT: U 48 LYS cc_start: 0.8595 (pttt) cc_final: 0.8224 (pttp) REVERT: U 63 LYS cc_start: 0.7881 (mttt) cc_final: 0.7564 (mtpp) outliers start: 22 outliers final: 14 residues processed: 268 average time/residue: 0.1276 time to fit residues: 47.4576 Evaluate side-chains 252 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 235 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 D residue 52 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 98 VAL 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: 6.9990 chunk 2 optimal weight: 4.9990 chunk 93 optimal weight: 30.0000 chunk 84 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 10.9990 chunk 19 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 0.0980 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.059632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.037932 restraints weight = 54101.111| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.47 r_work: 0.2566 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2563 r_free = 0.2563 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2563 r_free = 0.2563 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13069 Z= 0.220 Angle : 0.732 13.588 18813 Z= 0.417 Chirality : 0.050 0.241 2149 Planarity : 0.005 0.045 1438 Dihedral : 31.385 148.969 3909 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.81 % Allowed : 14.10 % Favored : 82.09 % 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: 0.08 (0.29), residues: 828 helix: 0.95 (0.22), residues: 553 sheet: -2.12 (0.99), residues: 19 loop : -1.72 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG U 42 TYR 0.022 0.002 TYR D 83 PHE 0.013 0.002 PHE E 67 TRP 0.007 0.003 TRP S 164 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.22 (13069) covalent geometry : angle 0.73240 / 0.42 (18813) hydrogen bonds : bond 0.06539 / 4.38 ( 746) hydrogen bonds : angle 3.30490 / 2.27 ( 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 263 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.312 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: A 50 GLU cc_start: 0.9347 (mt-10) cc_final: 0.9012 (mt-10) REVERT: A 94 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8734 (mt-10) REVERT: B 44 LYS cc_start: 0.9474 (ttpp) cc_final: 0.9259 (mtpt) REVERT: B 84 MET cc_start: 0.8886 (tpp) cc_final: 0.8663 (tpp) REVERT: C 92 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8285 (mt-10) REVERT: C 94 ASN cc_start: 0.9367 (OUTLIER) cc_final: 0.9141 (t0) REVERT: D 63 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8967 (m-40) REVERT: E 79 LYS cc_start: 0.8965 (tptp) cc_final: 0.8757 (tptp) REVERT: F 25 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8539 (m-40) REVERT: G 15 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8166 (tmmt) REVERT: G 38 ASN cc_start: 0.9071 (m-40) cc_final: 0.8806 (m-40) REVERT: G 56 GLU cc_start: 0.8940 (tt0) cc_final: 0.8548 (mt-10) REVERT: G 89 ASN cc_start: 0.9112 (m110) cc_final: 0.8513 (m110) REVERT: G 92 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8503 (mt-10) REVERT: G 112 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8617 (mm110) REVERT: H 59 MET cc_start: 0.9291 (tpp) cc_final: 0.8991 (tpp) REVERT: H 71 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8702 (tp30) REVERT: H 93 GLU cc_start: 0.8842 (mp0) cc_final: 0.8554 (mp0) REVERT: U 48 LYS cc_start: 0.8555 (pttt) cc_final: 0.8243 (pttp) REVERT: U 63 LYS cc_start: 0.7804 (mttt) cc_final: 0.7464 (mtpp) REVERT: U 73 LEU cc_start: 0.7748 (tp) cc_final: 0.7361 (tp) outliers start: 27 outliers final: 13 residues processed: 248 average time/residue: 0.1212 time to fit residues: 41.7115 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 : 0.357 ------------------------------------------------------------------------------- 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 D residue 63 ASN 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 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 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: 6.9990 chunk 105 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 47 optimal weight: 0.2980 chunk 44 optimal weight: 0.7980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 63 ASN 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 = 0.3467 r_free = 0.3467 target = 0.059961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.038803 restraints weight = 53777.346| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.43 r_work: 0.2597 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13069 Z= 0.156 Angle : 0.677 10.279 18813 Z= 0.393 Chirality : 0.048 0.254 2149 Planarity : 0.004 0.049 1438 Dihedral : 31.219 149.923 3908 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.53 % Allowed : 15.80 % Favored : 80.68 % 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: 0.56 (0.30), residues: 828 helix: 1.37 (0.22), residues: 553 sheet: -1.97 (1.02), residues: 19 loop : -1.69 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.018 0.001 TYR H 83 PHE 0.012 0.001 PHE E 67 TRP 0.005 0.003 TRP S 164 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (13069) covalent geometry : angle 0.67667 / 0.39 (18813) hydrogen bonds : bond 0.05898 / 4.00 ( 746) hydrogen bonds : angle 3.15161 / 2.16 ( 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 262 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9335 (mt-10) cc_final: 0.8970 (mt-10) REVERT: A 62 ILE cc_start: 0.9458 (mp) cc_final: 0.8560 (mp) REVERT: A 68 GLN cc_start: 0.9305 (tm-30) cc_final: 0.8688 (tm-30) REVERT: A 94 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8715 (mt-10) REVERT: A 106 ASP cc_start: 0.8560 (m-30) cc_final: 0.8279 (m-30) REVERT: B 84 MET cc_start: 0.8889 (tpp) cc_final: 0.8683 (tpp) REVERT: C 64 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8819 (tm-30) REVERT: E 79 LYS cc_start: 0.8880 (tptp) cc_final: 0.8594 (tptp) REVERT: E 120 MET cc_start: 0.8952 (mmm) cc_final: 0.8696 (mmm) REVERT: F 25 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8539 (m-40) REVERT: G 15 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8221 (tmmt) REVERT: G 56 GLU cc_start: 0.8880 (tt0) cc_final: 0.8473 (mt-10) REVERT: G 89 ASN cc_start: 0.9150 (m110) cc_final: 0.8529 (m110) REVERT: G 92 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8479 (mt-10) REVERT: G 112 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8598 (mm110) REVERT: H 59 MET cc_start: 0.9315 (tpp) cc_final: 0.9045 (tpp) REVERT: H 71 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8670 (tp30) REVERT: H 93 GLU cc_start: 0.8803 (mp0) cc_final: 0.8532 (mp0) REVERT: U 29 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8698 (mptt) REVERT: U 48 LYS cc_start: 0.8459 (pttt) cc_final: 0.8130 (pttp) REVERT: U 63 LYS cc_start: 0.7705 (mttt) cc_final: 0.7423 (mtpp) outliers start: 25 outliers final: 12 residues processed: 247 average time/residue: 0.1073 time to fit residues: 36.7148 Evaluate side-chains 246 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 233 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 D residue 63 ASN 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 G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain U residue 43 LEU Chi-restraints excluded: chain U residue 52 ASP 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: 10.0000 chunk 100 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 81 optimal weight: 40.0000 chunk 59 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.059428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.038171 restraints weight = 54452.422| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.44 r_work: 0.2580 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13069 Z= 0.189 Angle : 0.682 7.274 18813 Z= 0.393 Chirality : 0.048 0.248 2149 Planarity : 0.004 0.048 1438 Dihedral : 31.144 150.218 3908 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.53 % Allowed : 17.63 % Favored : 78.84 % 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: 0.92 (0.30), residues: 828 helix: 1.71 (0.22), residues: 551 sheet: -1.91 (1.04), residues: 19 loop : -1.66 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 74 TYR 0.022 0.002 TYR H 83 PHE 0.011 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 0.00373 / 0.19 (13069) covalent geometry : angle 0.68180 / 0.39 (18813) hydrogen bonds : bond 0.05945 / 4.00 ( 746) hydrogen bonds : angle 3.16195 / 2.17 ( 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 254 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9331 (mt-10) cc_final: 0.8977 (mt-10) REVERT: A 68 GLN cc_start: 0.9290 (tm-30) cc_final: 0.8672 (tm-30) REVERT: A 94 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8782 (mt-10) REVERT: A 106 ASP cc_start: 0.8530 (m-30) cc_final: 0.8273 (m-30) REVERT: B 44 LYS cc_start: 0.9354 (mtpt) cc_final: 0.9082 (mtpp) REVERT: B 84 MET cc_start: 0.8950 (tpp) cc_final: 0.8741 (tpp) REVERT: C 64 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8827 (tm-30) REVERT: C 92 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8137 (mt-10) REVERT: D 71 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8946 (tm-30) REVERT: E 79 LYS cc_start: 0.8903 (tptp) cc_final: 0.8560 (tptp) REVERT: E 120 MET cc_start: 0.9041 (mmm) cc_final: 0.8798 (mmm) REVERT: F 25 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8516 (m-40) REVERT: F 88 TYR cc_start: 0.9137 (m-10) cc_final: 0.8668 (m-10) REVERT: G 15 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8228 (tmmt) REVERT: G 56 GLU cc_start: 0.8920 (tt0) cc_final: 0.8516 (mt-10) REVERT: G 89 ASN cc_start: 0.9147 (m110) cc_final: 0.8551 (m110) REVERT: G 112 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8604 (mm110) REVERT: H 59 MET cc_start: 0.9326 (tpp) cc_final: 0.9072 (tpp) REVERT: H 83 TYR cc_start: 0.8443 (m-10) cc_final: 0.8242 (m-80) REVERT: H 93 GLU cc_start: 0.8827 (mp0) cc_final: 0.8502 (mp0) REVERT: U 29 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8707 (mptt) REVERT: U 63 LYS cc_start: 0.7702 (mttt) cc_final: 0.7444 (mtpp) outliers start: 25 outliers final: 15 residues processed: 241 average time/residue: 0.1154 time to fit residues: 38.9465 Evaluate side-chains 238 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 222 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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 47 GLN Chi-restraints excluded: chain H residue 91 SER 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: 1.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 45 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.059671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.038396 restraints weight = 54507.925| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.48 r_work: 0.2584 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2795 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= 0.166 Angle : 0.665 6.869 18813 Z= 0.386 Chirality : 0.047 0.256 2149 Planarity : 0.004 0.051 1438 Dihedral : 31.056 150.661 3908 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.95 % Allowed : 17.49 % Favored : 78.56 % 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: 1.16 (0.30), residues: 828 helix: 1.90 (0.22), residues: 552 sheet: -1.76 (1.04), residues: 19 loop : -1.61 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG U 74 TYR 0.022 0.002 TYR C 57 PHE 0.014 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 0.00319 / 0.17 (13069) covalent geometry : angle 0.66539 / 0.39 (18813) hydrogen bonds : bond 0.05720 / 3.86 ( 746) hydrogen bonds : angle 3.07479 / 2.12 ( 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 264 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9361 (mt-10) cc_final: 0.9018 (mt-10) REVERT: A 68 GLN cc_start: 0.9306 (tm-30) cc_final: 0.8797 (tm-30) REVERT: A 94 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8769 (mt-10) REVERT: A 106 ASP cc_start: 0.8581 (m-30) cc_final: 0.8368 (m-30) REVERT: B 44 LYS cc_start: 0.9381 (mtpt) cc_final: 0.9107 (mtpp) REVERT: B 84 MET cc_start: 0.8961 (tpp) cc_final: 0.8744 (tpp) REVERT: C 64 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8832 (tm-30) REVERT: C 92 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8008 (mt-10) REVERT: E 120 MET cc_start: 0.9050 (mmm) cc_final: 0.8812 (mmm) REVERT: F 25 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8478 (m-40) REVERT: F 88 TYR cc_start: 0.9191 (m-10) cc_final: 0.8775 (m-10) REVERT: G 15 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8221 (tmmt) REVERT: G 89 ASN cc_start: 0.9159 (m110) cc_final: 0.8558 (m110) REVERT: G 112 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8609 (mm110) REVERT: H 83 TYR cc_start: 0.8530 (m-10) cc_final: 0.8240 (m-80) REVERT: H 93 GLU cc_start: 0.8849 (mp0) cc_final: 0.8493 (mp0) REVERT: U 29 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8698 (mptt) REVERT: U 63 LYS cc_start: 0.7741 (mttt) cc_final: 0.7499 (mtpp) outliers start: 28 outliers final: 17 residues processed: 247 average time/residue: 0.1231 time to fit residues: 42.0813 Evaluate side-chains 245 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 41 VAL 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 F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR 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 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: 9.9990 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 81 optimal weight: 40.0000 chunk 91 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN C 104 GLN D 47 GLN D 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.059898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.038680 restraints weight = 53417.081| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.43 r_work: 0.2591 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2887 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= 0.163 Angle : 0.665 6.849 18813 Z= 0.385 Chirality : 0.046 0.255 2149 Planarity : 0.004 0.049 1438 Dihedral : 31.005 150.731 3908 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.53 % Allowed : 19.89 % Favored : 76.59 % 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: 1.29 (0.30), residues: 828 helix: 1.99 (0.22), residues: 552 sheet: -1.69 (1.03), residues: 19 loop : -1.54 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 74 TYR 0.021 0.001 TYR C 57 PHE 0.014 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 0.00318 / 0.16 (13069) covalent geometry : angle 0.66536 / 0.38 (18813) hydrogen bonds : bond 0.05671 / 3.82 ( 746) hydrogen bonds : angle 3.05528 / 2.10 ( 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 256 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9352 (mt-10) cc_final: 0.9010 (mt-10) REVERT: A 94 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8739 (mt-10) REVERT: B 44 LYS cc_start: 0.9385 (mtpt) cc_final: 0.9100 (mtpp) REVERT: B 84 MET cc_start: 0.8985 (tpp) cc_final: 0.8763 (tpp) REVERT: C 64 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8950 (tm-30) REVERT: C 92 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7986 (mt-10) REVERT: E 79 LYS cc_start: 0.8843 (tptm) cc_final: 0.8579 (tptp) REVERT: E 120 MET cc_start: 0.9051 (mmm) cc_final: 0.8836 (mmm) REVERT: F 25 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8490 (m-40) REVERT: F 62 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9224 (mp) REVERT: F 88 TYR cc_start: 0.9240 (m-10) cc_final: 0.8454 (m-80) REVERT: G 15 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8225 (tmmt) REVERT: G 38 ASN cc_start: 0.8966 (m-40) cc_final: 0.8749 (m-40) REVERT: G 56 GLU cc_start: 0.8969 (tt0) cc_final: 0.8483 (mt-10) REVERT: G 89 ASN cc_start: 0.9153 (m110) cc_final: 0.8565 (m110) REVERT: G 112 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8490 (mm110) REVERT: H 83 TYR cc_start: 0.8502 (m-10) cc_final: 0.8186 (m-80) REVERT: H 93 GLU cc_start: 0.8841 (mp0) cc_final: 0.8503 (mp0) REVERT: U 29 LYS cc_start: 0.9007 (mmmm) cc_final: 0.8710 (mptt) REVERT: U 63 LYS cc_start: 0.7719 (mttt) cc_final: 0.7507 (mtpp) outliers start: 25 outliers final: 15 residues processed: 240 average time/residue: 0.1271 time to fit residues: 41.9185 Evaluate side-chains 243 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 226 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 74 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 81 optimal weight: 50.0000 chunk 69 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 17 optimal weight: 0.2980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.059833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.038777 restraints weight = 53716.773| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.41 r_work: 0.2591 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13069 Z= 0.166 Angle : 0.670 6.830 18813 Z= 0.387 Chirality : 0.046 0.255 2149 Planarity : 0.004 0.051 1438 Dihedral : 30.971 150.733 3908 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.10 % Allowed : 20.73 % Favored : 76.16 % 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: 2.02 (0.22), residues: 552 sheet: -1.82 (1.01), residues: 19 loop : -1.48 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.024 0.001 TYR C 57 PHE 0.015 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 0.00328 / 0.17 (13069) covalent geometry : angle 0.66963 / 0.39 (18813) hydrogen bonds : bond 0.05629 / 3.79 ( 746) hydrogen bonds : angle 3.04537 / 2.09 ( 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 252 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8998 (mt-10) REVERT: A 94 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8735 (mt-10) REVERT: B 44 LYS cc_start: 0.9397 (mtpt) cc_final: 0.9107 (mtpp) REVERT: B 84 MET cc_start: 0.8990 (tpp) cc_final: 0.8770 (tpp) REVERT: C 64 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8962 (tm-30) REVERT: E 79 LYS cc_start: 0.8826 (tptm) cc_final: 0.8592 (tptp) REVERT: E 120 MET cc_start: 0.9054 (mmm) cc_final: 0.8843 (mmm) REVERT: F 25 ASN cc_start: 0.8984 (OUTLIER) cc_final: 0.8474 (m-40) REVERT: F 62 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9143 (mp) REVERT: F 88 TYR cc_start: 0.9255 (m-10) cc_final: 0.8476 (m-80) REVERT: G 15 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8224 (tmmt) REVERT: G 38 ASN cc_start: 0.8950 (m-40) cc_final: 0.8734 (m-40) REVERT: G 56 GLU cc_start: 0.8988 (tt0) cc_final: 0.8527 (mt-10) REVERT: G 89 ASN cc_start: 0.9153 (m110) cc_final: 0.8558 (m110) REVERT: H 83 TYR cc_start: 0.8510 (m-10) cc_final: 0.8194 (m-80) REVERT: H 93 GLU cc_start: 0.8842 (mp0) cc_final: 0.8495 (mp0) REVERT: U 29 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8708 (mptt) REVERT: U 63 LYS cc_start: 0.7719 (mttt) cc_final: 0.7481 (mtpp) outliers start: 22 outliers final: 16 residues processed: 239 average time/residue: 0.1321 time to fit residues: 43.5993 Evaluate side-chains 246 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 C residue 118 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 63 ASN 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 62 ILE Chi-restraints excluded: chain G residue 101 THR 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 43 LEU 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: 0.9980 chunk 16 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.059909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.038841 restraints weight = 53729.583| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.41 r_work: 0.2597 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13069 Z= 0.158 Angle : 0.674 6.820 18813 Z= 0.387 Chirality : 0.046 0.256 2149 Planarity : 0.004 0.049 1438 Dihedral : 30.934 150.635 3908 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.96 % Allowed : 21.16 % 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: 1.44 (0.30), residues: 828 helix: 2.08 (0.22), residues: 552 sheet: -1.72 (1.02), residues: 19 loop : -1.41 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 74 TYR 0.024 0.001 TYR C 57 PHE 0.015 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 0.00311 / 0.16 (13069) covalent geometry : angle 0.67350 / 0.39 (18813) hydrogen bonds : bond 0.05570 / 3.75 ( 746) hydrogen bonds : angle 3.02492 / 2.08 ( 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 252 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9331 (mt-10) cc_final: 0.8984 (mt-10) REVERT: A 94 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8761 (mm-30) REVERT: B 44 LYS cc_start: 0.9382 (mtpt) cc_final: 0.9093 (mtpp) REVERT: B 84 MET cc_start: 0.8983 (tpp) cc_final: 0.8763 (tpp) REVERT: C 64 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8945 (tm-30) REVERT: D 68 ASP cc_start: 0.9314 (t70) cc_final: 0.8948 (t0) REVERT: E 79 LYS cc_start: 0.8848 (tptm) cc_final: 0.8583 (tptp) REVERT: E 120 MET cc_start: 0.9052 (mmm) cc_final: 0.8845 (mmm) REVERT: F 25 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8478 (m-40) REVERT: F 88 TYR cc_start: 0.9267 (m-10) cc_final: 0.8528 (m-80) REVERT: G 15 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8225 (tmmt) REVERT: G 38 ASN cc_start: 0.8940 (m-40) cc_final: 0.8728 (m-40) REVERT: G 56 GLU cc_start: 0.8984 (tt0) cc_final: 0.8543 (mt-10) REVERT: G 89 ASN cc_start: 0.9148 (m110) cc_final: 0.8553 (m110) REVERT: H 83 TYR cc_start: 0.8468 (m-10) cc_final: 0.8129 (m-80) REVERT: H 93 GLU cc_start: 0.8835 (mp0) cc_final: 0.8501 (mp0) REVERT: U 6 LYS cc_start: 0.9143 (ttmt) cc_final: 0.8931 (ttmt) REVERT: U 29 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8707 (mptt) REVERT: U 33 LYS cc_start: 0.8539 (mtpp) cc_final: 0.8270 (mtpp) REVERT: U 63 LYS cc_start: 0.7708 (mttt) cc_final: 0.7508 (mtpp) outliers start: 21 outliers final: 15 residues processed: 240 average time/residue: 0.1335 time to fit residues: 44.0581 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 : 0.362 ------------------------------------------------------------------------------- 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 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 62 ILE Chi-restraints excluded: chain G residue 101 THR 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 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: 0.9990 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 94 optimal weight: 50.0000 chunk 102 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.060067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.038928 restraints weight = 53885.680| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.42 r_work: 0.2600 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13069 Z= 0.159 Angle : 0.675 7.923 18813 Z= 0.388 Chirality : 0.046 0.256 2149 Planarity : 0.004 0.051 1438 Dihedral : 30.895 150.334 3908 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.68 % Allowed : 21.44 % 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: 1.49 (0.31), residues: 828 helix: 2.09 (0.22), residues: 555 sheet: -1.64 (1.02), residues: 19 loop : -1.36 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.027 0.001 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 0.00312 / 0.16 (13069) covalent geometry : angle 0.67519 / 0.39 (18813) hydrogen bonds : bond 0.05539 / 3.73 ( 746) hydrogen bonds : angle 3.02178 / 2.07 ( 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 253 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 234 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: 0.9340 (mt-10) cc_final: 0.8998 (mt-10) REVERT: B 44 LYS cc_start: 0.9359 (mtpt) cc_final: 0.9069 (mtpp) REVERT: B 84 MET cc_start: 0.8987 (tpp) cc_final: 0.8767 (tpp) REVERT: C 64 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8936 (tm-30) REVERT: C 89 ASN cc_start: 0.9436 (m-40) cc_final: 0.9042 (m110) REVERT: D 46 LYS cc_start: 0.9377 (mmmt) cc_final: 0.9156 (mmmt) REVERT: D 68 ASP cc_start: 0.9285 (t70) cc_final: 0.8905 (t0) REVERT: E 79 LYS cc_start: 0.8880 (tptm) cc_final: 0.8626 (tptp) REVERT: E 120 MET cc_start: 0.9066 (mmm) cc_final: 0.8855 (mmm) REVERT: F 25 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8482 (m-40) REVERT: F 88 TYR cc_start: 0.9221 (m-10) cc_final: 0.8495 (m-80) REVERT: G 15 LYS cc_start: 0.8709 (ttmm) cc_final: 0.8222 (tmmt) REVERT: G 56 GLU cc_start: 0.8956 (tt0) cc_final: 0.8524 (mt-10) REVERT: G 89 ASN cc_start: 0.9146 (m110) cc_final: 0.8545 (m110) REVERT: H 71 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8722 (tp30) REVERT: H 83 TYR cc_start: 0.8445 (m-10) cc_final: 0.8025 (m-80) REVERT: H 93 GLU cc_start: 0.8843 (mp0) cc_final: 0.8507 (mp0) REVERT: H 105 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8195 (tp30) REVERT: U 29 LYS cc_start: 0.9011 (mmmm) cc_final: 0.8740 (mptt) outliers start: 19 outliers final: 14 residues processed: 244 average time/residue: 0.1284 time to fit residues: 43.0247 Evaluate side-chains 243 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 6 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 17 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.060288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.039202 restraints weight = 53561.265| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.41 r_work: 0.2611 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13069 Z= 0.148 Angle : 0.674 7.233 18813 Z= 0.387 Chirality : 0.045 0.257 2149 Planarity : 0.004 0.049 1438 Dihedral : 30.853 149.791 3908 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % 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: 1.58 (0.31), residues: 828 helix: 2.15 (0.22), residues: 554 sheet: -1.56 (1.05), residues: 19 loop : -1.31 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 42 TYR 0.025 0.001 TYR C 57 PHE 0.017 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 0.00290 / 0.15 (13069) covalent geometry : angle 0.67352 / 0.39 (18813) hydrogen bonds : bond 0.05441 / 3.67 ( 746) hydrogen bonds : angle 2.98601 / 2.05 ( 1855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3449.92 seconds wall clock time: 59 minutes 33.95 seconds (3573.95 seconds total)