Starting phenix.real_space_refine on Sat Sep 12 07:31:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oh9_12897/09_2026/7oh9_12897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oh9_12897/09_2026/7oh9_12897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oh9_12897/09_2026/7oh9_12897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oh9_12897/09_2026/7oh9_12897.map" model { file = "/net/cci-nas-00/data/ceres_data/7oh9_12897/09_2026/7oh9_12897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oh9_12897/09_2026/7oh9_12897.cif" } resolution = 3.0 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 25 5.16 5 C 8612 2.51 5 N 2782 2.21 5 O 3390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15099 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1439 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Conformer: "B" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} bond proxies already assigned to first conformer: 1417 Chain: "L" Number of atoms: 823 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 96, 796 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'TRANS': 95} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 96, 796 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'TRANS': 95} Chain breaks: 2 bond proxies already assigned to first conformer: 775 Chain: "M" Number of atoms: 815 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 104, 807 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 104, 807 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 805 Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N ALEU K 134 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU K 134 " occ=0.50 residue: pdb=" N ALYS K 138 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS K 138 " occ=0.50 residue: pdb=" N ASER K 184 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER K 184 " occ=0.50 residue: pdb=" N AGLU L 11 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU L 11 " occ=0.50 residue: pdb=" N AGLN L 280 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN L 280 " occ=0.50 residue: pdb=" N AGLU L 282 " occ=0.60 ... (16 atoms not shown) pdb=" OE2BGLU L 282 " occ=0.40 residue: pdb=" N AILE M 79 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE M 79 " occ=0.50 Time building chain proxies: 3.34, per 1000 atoms: 0.22 Number of scatterers: 15099 At special positions: 0 Unit cell: (93.45, 129.15, 142.8, 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 25 16.00 P 290 15.00 O 3390 8.00 N 2782 7.00 C 8612 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: 0.93 Conformation dependent library (CDL) restraints added in 548.6 milliseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 60.5% alpha, 13.3% beta 143 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.022A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.502A 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 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.380A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.614A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.883A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.566A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.701A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 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 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.269A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 Processing helix chain 'K' and resid 81 through 89 removed outlier: 4.191A pdb=" N VAL K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 147 Processing helix chain 'K' and resid 171 through 179 Processing helix chain 'K' and resid 219 through 236 removed outlier: 3.615A pdb=" N ILE K 223 " --> pdb=" O GLN K 219 " (cutoff:3.500A) Proline residue: K 232 - end of helix Processing helix chain 'L' and resid 4 through 19 Processing helix chain 'L' and resid 20 through 27 removed outlier: 4.665A pdb=" N ASP L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 47 Processing helix chain 'M' and resid 8 through 12 removed outlier: 4.298A pdb=" N ARG M 11 " --> pdb=" O GLU M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 29 Processing helix chain 'M' and resid 33 through 55 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.092A 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: 6.463A 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: 7.072A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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: 6.999A 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: 7.235A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 'K' and resid 93 through 95 removed outlier: 6.189A pdb=" N GLU K 93 " --> pdb=" O ALA K 101 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ALA K 101 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN K 95 " --> pdb=" O PHE K 99 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR K 111 " --> pdb=" O ILE K 106 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL K 122 " --> pdb=" O LEU K 114 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE K 70 " --> pdb=" O GLY K 125 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL K 161 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE K 70 " --> pdb=" O ASN K 159 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN K 159 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA K 72 " --> pdb=" O ILE K 157 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE K 157 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL K 74 " --> pdb=" O PHE K 155 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE K 155 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 243 through 253 removed outlier: 7.512A pdb=" N LEU L 243 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL L 267 " --> pdb=" O LEU L 243 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU L 245 " --> pdb=" O GLY L 265 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY L 265 " --> pdb=" O LEU L 245 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER L 261 " --> pdb=" O ASP L 249 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL L 251 " --> pdb=" O LYS L 259 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS L 259 " --> pdb=" O VAL L 251 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP L 264 " --> pdb=" O GLN L 277 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLN L 277 " --> pdb=" O ASP L 264 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL L 266 " --> pdb=" O THR L 275 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR L 275 " --> pdb=" O VAL L 266 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU M 60 " --> pdb=" O PHE L 276 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LYS L 278 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL M 62 " --> pdb=" O LYS L 278 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N AGLN L 280 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLY M 64 " --> pdb=" O AGLN L 280 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N AGLU L 282 " --> pdb=" O GLY M 64 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU M 66 " --> pdb=" O AGLU L 282 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LYS M 59 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL M 87 " --> pdb=" O LYS M 59 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR M 61 " --> pdb=" O VAL M 85 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL M 85 " --> pdb=" O THR M 61 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS M 63 " --> pdb=" O CYS M 83 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N CYS M 83 " --> pdb=" O LYS M 63 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N AILE M 79 " --> pdb=" O ASP M 67 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR M 69 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR M 77 " --> pdb=" O TYR M 69 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE M 71 " --> pdb=" O VAL M 75 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL M 75 " --> pdb=" O PHE M 71 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL M 75 " --> pdb=" O CYS M 116 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N CYS M 116 " --> pdb=" O VAL M 75 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR M 77 " --> pdb=" O VAL M 114 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL M 114 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N AILE M 79 " --> pdb=" O ARG M 112 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ARG M 112 " --> pdb=" O AILE M 79 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS M 81 " --> pdb=" O LYS M 110 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LYS M 110 " --> pdb=" O LYS M 81 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS M 116 " --> pdb=" O CYS L 246 " (cutoff:3.500A) 566 hydrogen bonds defined for protein. 1669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 365 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2919 1.33 - 1.45: 4821 1.45 - 1.57: 7592 1.57 - 1.69: 579 1.69 - 1.81: 41 Bond restraints: 15952 Sorted by residual: bond pdb=" C3' DG J 8 " pdb=" O3' DG J 8 " ideal model delta sigma weight residual 1.435 1.378 0.057 1.30e-02 5.92e+03 1.89e+01 bond pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.07e+01 bond pdb=" C3' DG J -22 " pdb=" C2' DG J -22 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DA J 16 " pdb=" O3' DA J 16 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" C3' DC I 7 " pdb=" O3' DC I 7 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 1.01e+01 ... (remaining 15947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 22434 2.73 - 5.45: 306 5.45 - 8.18: 36 8.18 - 10.90: 10 10.90 - 13.63: 2 Bond angle restraints: 22788 Sorted by residual: angle pdb=" O4' DT I -26 " pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 106.00 102.58 3.42 6.00e-01 2.78e+00 3.24e+01 angle pdb=" N GLU L 20 " pdb=" CA GLU L 20 " pdb=" CB GLU L 20 " ideal model delta sigma weight residual 110.53 118.18 -7.65 1.47e+00 4.63e-01 2.71e+01 angle pdb=" C ASN L 19 " pdb=" N GLU L 20 " pdb=" CA GLU L 20 " ideal model delta sigma weight residual 121.92 113.28 8.64 1.73e+00 3.34e-01 2.50e+01 angle pdb=" O5' DA J 28 " pdb=" C5' DA J 28 " pdb=" C4' DA J 28 " ideal model delta sigma weight residual 109.40 113.36 -3.96 8.00e-01 1.56e+00 2.45e+01 angle pdb=" CA GLU C 64 " pdb=" CB GLU C 64 " pdb=" CG GLU C 64 " ideal model delta sigma weight residual 114.10 123.46 -9.36 2.00e+00 2.50e-01 2.19e+01 ... (remaining 22783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.02: 6335 19.02 - 38.04: 1221 38.04 - 57.06: 1180 57.06 - 76.08: 152 76.08 - 95.10: 11 Dihedral angle restraints: 8899 sinusoidal: 5541 harmonic: 3358 Sorted by residual: dihedral pdb=" CA ASN L 19 " pdb=" C ASN L 19 " pdb=" N GLU L 20 " pdb=" CA GLU L 20 " ideal model delta harmonic sigma weight residual 180.00 145.51 34.49 0 5.00e+00 4.00e-02 4.76e+01 dihedral pdb=" CA GLU K 186 " pdb=" C GLU K 186 " pdb=" N PRO K 187 " pdb=" CA PRO K 187 " ideal model delta harmonic sigma weight residual -180.00 -146.31 -33.69 0 5.00e+00 4.00e-02 4.54e+01 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -152.56 -27.44 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 8896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2092 0.069 - 0.139: 477 0.139 - 0.208: 30 0.208 - 0.277: 3 0.277 - 0.347: 4 Chirality restraints: 2606 Sorted by residual: chirality pdb=" CG LEU L 262 " pdb=" CB LEU L 262 " pdb=" CD1 LEU L 262 " pdb=" CD2 LEU L 262 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CG LEU M 19 " pdb=" CB LEU M 19 " pdb=" CD1 LEU M 19 " pdb=" CD2 LEU M 19 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CG LEU A 61 " pdb=" CB LEU A 61 " pdb=" CD1 LEU A 61 " pdb=" CD2 LEU A 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 2603 not shown) Planarity restraints: 1879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN M 55 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ASN M 55 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN M 55 " 0.021 2.00e-02 2.50e+03 pdb=" N THR M 56 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 64 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" CD GLU C 64 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU C 64 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU C 64 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.02e+00 pdb=" N PRO C 80 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.034 5.00e-02 4.00e+02 ... (remaining 1876 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2547 2.77 - 3.30: 13473 3.30 - 3.83: 30580 3.83 - 4.37: 35913 4.37 - 4.90: 51531 Nonbonded interactions: 134044 Sorted by model distance: nonbonded pdb=" O ASP M 21 " pdb=" OG1 THR M 25 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR M 7 " pdb=" OD1 ASN M 117 " model vdw 2.250 3.040 nonbonded pdb=" OE1 GLU L 32 " pdb=" NE2 GLN L 36 " model vdw 2.293 3.120 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.294 3.040 nonbonded pdb=" O ALA L 4 " pdb=" OG SER L 7 " model vdw 2.295 3.040 ... (remaining 134039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 122) 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.040 Find NCS groups from input model: 0.140 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:8.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 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 : 0.007 0.108 15952 Z= 0.574 Angle : 0.946 13.630 22788 Z= 0.709 Chirality : 0.055 0.347 2606 Planarity : 0.006 0.066 1879 Dihedral : 25.973 95.104 6729 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: -0.54 (0.23), residues: 1136 helix: 0.08 (0.18), residues: 678 sheet: 0.18 (0.49), residues: 120 loop : -1.25 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 83 TYR 0.038 0.003 TYR G 57 PHE 0.031 0.002 PHE M 78 TRP 0.031 0.003 TRP M 76 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00749 / 0.57 (15952) covalent geometry : angle 0.94636 / 0.71 (22788) hydrogen bonds : bond 0.11791 / 8.03 ( 931) hydrogen bonds : angle 4.94666 / 3.58 ( 2399) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 LYS cc_start: 0.8631 (tptm) cc_final: 0.8424 (mmmt) REVERT: D 68 GLU cc_start: 0.7644 (tp30) cc_final: 0.7443 (tp30) REVERT: D 90 GLU cc_start: 0.8280 (mp0) cc_final: 0.8027 (mp0) REVERT: F 59 LYS cc_start: 0.8707 (tttm) cc_final: 0.8500 (ttpp) REVERT: H 65 ASP cc_start: 0.8494 (t70) cc_final: 0.8240 (t0) REVERT: K 88 HIS cc_start: 0.9195 (m-70) cc_final: 0.8874 (m-70) REVERT: K 104 MET cc_start: 0.8851 (pmm) cc_final: 0.8533 (ppp) REVERT: K 139 TYR cc_start: 0.8699 (m-80) cc_final: 0.8089 (m-10) REVERT: K 212 ILE cc_start: 0.9074 (mm) cc_final: 0.8829 (pp) REVERT: K 221 GLU cc_start: 0.8992 (tp30) cc_final: 0.8324 (tp30) REVERT: K 222 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8264 (mt-10) REVERT: K 224 TYR cc_start: 0.9266 (m-10) cc_final: 0.8985 (m-10) REVERT: K 225 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8704 (mm110) REVERT: L 248 TYR cc_start: 0.9024 (p90) cc_final: 0.8321 (p90) REVERT: M 78 PHE cc_start: 0.9298 (m-80) cc_final: 0.8918 (m-80) outliers start: 0 outliers final: 1 residues processed: 300 average time/residue: 0.6873 time to fit residues: 222.9420 Evaluate side-chains 260 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.0770 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 25 ASN C 73 ASN C 104 GLN C 112 GLN D 92 GLN G 94 ASN H 44 GLN H 46 HIS K 158 GLN ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.096616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.057232 restraints weight = 119050.586| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.33 r_work: 0.2565 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 71 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15952 Z= 0.181 Angle : 0.741 11.269 22788 Z= 0.410 Chirality : 0.048 0.234 2606 Planarity : 0.005 0.052 1879 Dihedral : 29.992 108.102 4458 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.74 % Allowed : 15.06 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % 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: 0.25 (0.23), residues: 1136 helix: 0.95 (0.19), residues: 687 sheet: -0.18 (0.49), residues: 112 loop : -1.25 (0.29), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 30 TYR 0.046 0.002 TYR L 10 PHE 0.026 0.002 PHE M 44 TRP 0.020 0.004 TRP L 258 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.18 (15952) covalent geometry : angle 0.74138 / 0.41 (22788) hydrogen bonds : bond 0.04706 / 3.15 ( 931) hydrogen bonds : angle 3.94903 / 2.90 ( 2399) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 276 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8981 (pm20) cc_final: 0.8422 (pm20) REVERT: A 123 ASP cc_start: 0.8923 (m-30) cc_final: 0.8606 (m-30) REVERT: D 31 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8725 (mptt) REVERT: D 90 GLU cc_start: 0.9131 (mp0) cc_final: 0.8924 (mp0) REVERT: D 105 LYS cc_start: 0.9046 (ptpp) cc_final: 0.8726 (pttm) REVERT: E 120 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8777 (mtm) REVERT: F 85 ASP cc_start: 0.8902 (m-30) cc_final: 0.8592 (m-30) REVERT: H 53 SER cc_start: 0.9342 (OUTLIER) cc_final: 0.8914 (p) REVERT: H 65 ASP cc_start: 0.9234 (t70) cc_final: 0.8941 (t0) REVERT: H 82 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8973 (mppt) REVERT: K 88 HIS cc_start: 0.9508 (m-70) cc_final: 0.9055 (m-70) REVERT: K 91 ASN cc_start: 0.8806 (m-40) cc_final: 0.8472 (m-40) REVERT: K 104 MET cc_start: 0.8825 (pmm) cc_final: 0.8601 (ppp) REVERT: K 121 MET cc_start: 0.8752 (ppp) cc_final: 0.8486 (ppp) REVERT: K 139 TYR cc_start: 0.8728 (m-80) cc_final: 0.7556 (m-80) REVERT: K 221 GLU cc_start: 0.9168 (tp30) cc_final: 0.8875 (tp30) REVERT: K 222 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8520 (mt-10) REVERT: L 248 TYR cc_start: 0.9157 (p90) cc_final: 0.8455 (p90) REVERT: M 76 TRP cc_start: 0.8551 (m100) cc_final: 0.8270 (m100) outliers start: 17 outliers final: 4 residues processed: 281 average time/residue: 0.6325 time to fit residues: 193.6767 Evaluate side-chains 272 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 265 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain M residue 42 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 62 optimal weight: 2.9990 chunk 73 optimal weight: 40.0000 chunk 87 optimal weight: 30.0000 chunk 57 optimal weight: 4.9990 chunk 85 optimal weight: 40.0000 chunk 102 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 133 optimal weight: 40.0000 chunk 104 optimal weight: 30.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN C 38 ASN C 104 GLN G 94 ASN H 44 GLN H 46 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.096498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.057115 restraints weight = 133923.017| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.58 r_work: 0.2550 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15952 Z= 0.179 Angle : 0.715 12.093 22788 Z= 0.396 Chirality : 0.047 0.229 2606 Planarity : 0.005 0.049 1879 Dihedral : 29.943 112.810 4456 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.38 % Allowed : 17.52 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % 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: 0.78 (0.24), residues: 1136 helix: 1.34 (0.19), residues: 690 sheet: 0.13 (0.46), residues: 130 loop : -1.07 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 29 TYR 0.041 0.002 TYR L 10 PHE 0.026 0.002 PHE M 44 TRP 0.033 0.004 TRP L 42 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (15952) covalent geometry : angle 0.71512 / 0.40 (22788) hydrogen bonds : bond 0.04445 / 2.97 ( 931) hydrogen bonds : angle 3.70624 / 2.70 ( 2399) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 265 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8375 (tm-30) REVERT: D 31 LYS cc_start: 0.9148 (mmmm) cc_final: 0.8841 (mptt) REVERT: D 90 GLU cc_start: 0.9166 (mp0) cc_final: 0.8913 (mp0) REVERT: E 120 MET cc_start: 0.9356 (OUTLIER) cc_final: 0.8858 (mtm) REVERT: G 94 ASN cc_start: 0.9452 (t0) cc_final: 0.9176 (t160) REVERT: H 31 LYS cc_start: 0.8168 (mppt) cc_final: 0.7880 (mppt) REVERT: H 65 ASP cc_start: 0.9269 (t70) cc_final: 0.8955 (t0) REVERT: H 82 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8959 (mppt) REVERT: K 69 ASN cc_start: 0.9308 (t0) cc_final: 0.8646 (t160) REVERT: K 88 HIS cc_start: 0.9564 (m-70) cc_final: 0.9029 (m-70) REVERT: K 121 MET cc_start: 0.8856 (ppp) cc_final: 0.8460 (ppp) REVERT: K 221 GLU cc_start: 0.9212 (tp30) cc_final: 0.8903 (tp30) REVERT: L 20 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8039 (pm20) REVERT: L 248 TYR cc_start: 0.9153 (p90) cc_final: 0.8433 (p90) outliers start: 33 outliers final: 18 residues processed: 275 average time/residue: 0.6477 time to fit residues: 193.2780 Evaluate side-chains 277 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 255 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 105 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 86 optimal weight: 50.0000 chunk 50 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 23 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN B 25 ASN C 104 GLN E 125 GLN H 44 GLN H 46 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.094960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.055307 restraints weight = 108380.395| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.20 r_work: 0.2512 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15952 Z= 0.278 Angle : 0.765 13.437 22788 Z= 0.412 Chirality : 0.049 0.235 2606 Planarity : 0.005 0.048 1879 Dihedral : 30.096 115.726 4456 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.48 % Allowed : 18.95 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % 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: 0.86 (0.24), residues: 1136 helix: 1.42 (0.19), residues: 690 sheet: 0.34 (0.48), residues: 123 loop : -1.14 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 27 TYR 0.040 0.002 TYR L 10 PHE 0.018 0.002 PHE M 44 TRP 0.041 0.006 TRP L 42 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.28 (15952) covalent geometry : angle 0.76547 / 0.41 (22788) hydrogen bonds : bond 0.04998 / 3.30 ( 931) hydrogen bonds : angle 3.69695 / 2.69 ( 2399) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 258 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9099 (m-30) cc_final: 0.8797 (m-30) REVERT: D 31 LYS cc_start: 0.9163 (mmmm) cc_final: 0.8885 (mptt) REVERT: D 90 GLU cc_start: 0.9146 (mp0) cc_final: 0.8764 (mp0) REVERT: D 105 LYS cc_start: 0.9101 (ptpp) cc_final: 0.8775 (pttm) REVERT: G 94 ASN cc_start: 0.9496 (t0) cc_final: 0.9251 (t160) REVERT: H 65 ASP cc_start: 0.9262 (t70) cc_final: 0.8911 (t0) REVERT: H 82 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8998 (mppt) REVERT: K 69 ASN cc_start: 0.9254 (t0) cc_final: 0.8649 (t160) REVERT: K 88 HIS cc_start: 0.9547 (m-70) cc_final: 0.8995 (m-70) REVERT: K 121 MET cc_start: 0.8822 (ppp) cc_final: 0.8417 (ppp) REVERT: K 221 GLU cc_start: 0.9263 (tp30) cc_final: 0.8439 (tp30) REVERT: K 225 GLN cc_start: 0.9333 (mm-40) cc_final: 0.8980 (mm110) REVERT: L 248 TYR cc_start: 0.9122 (p90) cc_final: 0.8388 (p90) outliers start: 34 outliers final: 21 residues processed: 269 average time/residue: 0.6628 time to fit residues: 193.4293 Evaluate side-chains 274 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 252 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 236 GLU Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 129 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN C 104 GLN H 44 GLN H 46 HIS ** K 159 ASN ** 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 = 0.3706 r_free = 0.3706 target = 0.096743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.057774 restraints weight = 107875.541| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.23 r_work: 0.2576 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15952 Z= 0.159 Angle : 0.712 13.197 22788 Z= 0.390 Chirality : 0.046 0.367 2606 Planarity : 0.004 0.045 1879 Dihedral : 29.925 120.138 4456 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.25 % Allowed : 21.00 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % 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: 1.09 (0.25), residues: 1136 helix: 1.59 (0.19), residues: 692 sheet: 0.33 (0.48), residues: 122 loop : -0.99 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 30 TYR 0.037 0.002 TYR L 10 PHE 0.020 0.001 PHE M 44 TRP 0.044 0.005 TRP L 42 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (15952) covalent geometry : angle 0.71165 / 0.39 (22788) hydrogen bonds : bond 0.04088 / 2.71 ( 931) hydrogen bonds : angle 3.56770 / 2.60 ( 2399) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 268 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9013 (m-30) cc_final: 0.8761 (m-30) REVERT: D 31 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8930 (mptt) REVERT: D 90 GLU cc_start: 0.9116 (mp0) cc_final: 0.8621 (mp0) REVERT: D 105 LYS cc_start: 0.9009 (ptpp) cc_final: 0.8716 (pttm) REVERT: G 94 ASN cc_start: 0.9448 (t0) cc_final: 0.9204 (t160) REVERT: H 65 ASP cc_start: 0.9264 (t70) cc_final: 0.8953 (t0) REVERT: H 73 GLU cc_start: 0.8956 (tp30) cc_final: 0.8748 (tp30) REVERT: H 76 ARG cc_start: 0.8861 (mtm-85) cc_final: 0.8485 (mtm110) REVERT: K 69 ASN cc_start: 0.9180 (t0) cc_final: 0.8597 (t160) REVERT: K 88 HIS cc_start: 0.9537 (m-70) cc_final: 0.8988 (m-70) REVERT: K 111 THR cc_start: 0.9415 (t) cc_final: 0.9202 (t) REVERT: K 121 MET cc_start: 0.8858 (ppp) cc_final: 0.8485 (ppp) REVERT: K 219 GLN cc_start: 0.8028 (pp30) cc_final: 0.7255 (pp30) REVERT: K 221 GLU cc_start: 0.9206 (tp30) cc_final: 0.8171 (tp30) REVERT: K 222 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8300 (mt-10) REVERT: K 225 GLN cc_start: 0.9293 (mm-40) cc_final: 0.8955 (mm110) REVERT: L 248 TYR cc_start: 0.9119 (p90) cc_final: 0.8437 (p90) outliers start: 22 outliers final: 11 residues processed: 275 average time/residue: 0.6469 time to fit residues: 193.1441 Evaluate side-chains 270 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 259 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 92 optimal weight: 20.0000 chunk 99 optimal weight: 50.0000 chunk 83 optimal weight: 20.0000 chunk 135 optimal weight: 0.3980 chunk 133 optimal weight: 40.0000 chunk 108 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 104 GLN G 73 ASN H 44 GLN H 46 HIS ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 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 = 0.3721 r_free = 0.3721 target = 0.097467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.058591 restraints weight = 130521.311| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.52 r_work: 0.2594 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15952 Z= 0.141 Angle : 0.694 13.788 22788 Z= 0.384 Chirality : 0.045 0.277 2606 Planarity : 0.004 0.045 1879 Dihedral : 29.757 122.689 4456 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.25 % Allowed : 21.52 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % 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: 1.26 (0.25), residues: 1136 helix: 1.74 (0.19), residues: 692 sheet: 0.20 (0.49), residues: 122 loop : -0.87 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.032 0.002 TYR L 10 PHE 0.021 0.001 PHE M 44 TRP 0.035 0.005 TRP L 42 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (15952) covalent geometry : angle 0.69446 / 0.38 (22788) hydrogen bonds : bond 0.03946 / 2.60 ( 931) hydrogen bonds : angle 3.47999 / 2.53 ( 2399) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 273 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.9147 (mtt-85) cc_final: 0.8875 (mtt90) REVERT: D 31 LYS cc_start: 0.9187 (mmmm) cc_final: 0.8906 (mptt) REVERT: D 90 GLU cc_start: 0.9119 (mp0) cc_final: 0.8675 (mp0) REVERT: E 57 SER cc_start: 0.9261 (t) cc_final: 0.9032 (p) REVERT: G 94 ASN cc_start: 0.9430 (t0) cc_final: 0.9199 (t160) REVERT: H 65 ASP cc_start: 0.9283 (t70) cc_final: 0.8989 (t0) REVERT: H 73 GLU cc_start: 0.8988 (tp30) cc_final: 0.8696 (tp30) REVERT: H 76 ARG cc_start: 0.8817 (mtm-85) cc_final: 0.8419 (mtm110) REVERT: K 69 ASN cc_start: 0.9207 (t0) cc_final: 0.8666 (t160) REVERT: K 88 HIS cc_start: 0.9552 (m-70) cc_final: 0.9010 (m-70) REVERT: K 111 THR cc_start: 0.9405 (t) cc_final: 0.9204 (t) REVERT: K 121 MET cc_start: 0.8962 (ppp) cc_final: 0.8530 (ppp) REVERT: K 221 GLU cc_start: 0.9161 (tp30) cc_final: 0.8268 (tp30) REVERT: K 225 GLN cc_start: 0.9290 (mm-40) cc_final: 0.8940 (mm110) REVERT: L 248 TYR cc_start: 0.9100 (p90) cc_final: 0.8405 (p90) outliers start: 22 outliers final: 12 residues processed: 281 average time/residue: 0.6178 time to fit residues: 189.0970 Evaluate side-chains 274 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 262 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 114 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 135 optimal weight: 0.0170 chunk 115 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 overall best weight: 2.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN C 104 GLN G 38 ASN H 44 GLN H 46 HIS ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.096362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.057031 restraints weight = 122974.926| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.44 r_work: 0.2558 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2562 r_free = 0.2562 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2562 r_free = 0.2562 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 95 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 15952 Z= 0.194 Angle : 0.733 13.313 22788 Z= 0.397 Chirality : 0.046 0.263 2606 Planarity : 0.004 0.045 1879 Dihedral : 29.879 124.313 4456 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.15 % Allowed : 22.54 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % 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: 1.25 (0.25), residues: 1136 helix: 1.78 (0.19), residues: 691 sheet: 0.20 (0.49), residues: 118 loop : -0.98 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 30 TYR 0.036 0.002 TYR K 94 PHE 0.020 0.002 PHE M 44 TRP 0.036 0.005 TRP M 76 HIS 0.004 0.001 HIS K 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (15952) covalent geometry : angle 0.73299 / 0.40 (22788) hydrogen bonds : bond 0.04270 / 2.81 ( 931) hydrogen bonds : angle 3.51915 / 2.54 ( 2399) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 262 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 LYS cc_start: 0.9156 (mmmm) cc_final: 0.8921 (mptt) REVERT: D 90 GLU cc_start: 0.9143 (mp0) cc_final: 0.8643 (mp0) REVERT: D 105 LYS cc_start: 0.9051 (ptpp) cc_final: 0.8704 (pttm) REVERT: E 125 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8632 (mm-40) REVERT: F 53 GLU cc_start: 0.9020 (tp30) cc_final: 0.8810 (tp30) REVERT: G 94 ASN cc_start: 0.9444 (t0) cc_final: 0.9212 (t160) REVERT: H 65 ASP cc_start: 0.9285 (t70) cc_final: 0.8980 (t0) REVERT: H 73 GLU cc_start: 0.8975 (tp30) cc_final: 0.8567 (tp30) REVERT: H 76 ARG cc_start: 0.8890 (mtm-85) cc_final: 0.8412 (mtm110) REVERT: K 69 ASN cc_start: 0.9199 (t0) cc_final: 0.8688 (t160) REVERT: K 88 HIS cc_start: 0.9557 (m-70) cc_final: 0.9022 (m-70) REVERT: K 121 MET cc_start: 0.9052 (ppp) cc_final: 0.8583 (ppp) REVERT: K 219 GLN cc_start: 0.7992 (pp30) cc_final: 0.7504 (pp30) REVERT: K 221 GLU cc_start: 0.9247 (tp30) cc_final: 0.8248 (tp30) REVERT: K 222 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8490 (pt0) REVERT: K 225 GLN cc_start: 0.9334 (mm-40) cc_final: 0.8971 (mm110) REVERT: K 240 MET cc_start: 0.7045 (ttt) cc_final: 0.6577 (tpp) outliers start: 21 outliers final: 15 residues processed: 270 average time/residue: 0.6246 time to fit residues: 183.9563 Evaluate side-chains 269 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 253 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 87 optimal weight: 30.0000 chunk 124 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN C 104 GLN G 73 ASN H 44 GLN H 46 HIS K 88 HIS ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 179 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.096205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.056738 restraints weight = 138374.309| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.62 r_work: 0.2543 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 95 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 95 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 15952 Z= 0.198 Angle : 0.729 16.764 22788 Z= 0.395 Chirality : 0.046 0.240 2606 Planarity : 0.004 0.044 1879 Dihedral : 29.940 126.490 4456 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.46 % Allowed : 22.85 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % 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: 1.21 (0.25), residues: 1136 helix: 1.74 (0.19), residues: 691 sheet: 0.20 (0.49), residues: 118 loop : -0.96 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 30 TYR 0.034 0.002 TYR L 10 PHE 0.021 0.002 PHE M 44 TRP 0.037 0.005 TRP M 76 HIS 0.006 0.001 HIS K 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 (15952) covalent geometry : angle 0.72922 / 0.40 (22788) hydrogen bonds : bond 0.04191 / 2.75 ( 931) hydrogen bonds : angle 3.52043 / 2.53 ( 2399) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 258 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8930 (mptt) REVERT: D 90 GLU cc_start: 0.9149 (mp0) cc_final: 0.8647 (mp0) REVERT: D 105 LYS cc_start: 0.9034 (ptpp) cc_final: 0.8730 (pttm) REVERT: E 125 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8642 (mm-40) REVERT: F 53 GLU cc_start: 0.9020 (tp30) cc_final: 0.8802 (tp30) REVERT: G 94 ASN cc_start: 0.9453 (t0) cc_final: 0.9224 (t160) REVERT: H 65 ASP cc_start: 0.9290 (t70) cc_final: 0.8997 (t0) REVERT: K 69 ASN cc_start: 0.9166 (t0) cc_final: 0.8685 (t160) REVERT: K 88 HIS cc_start: 0.9475 (m90) cc_final: 0.8990 (m-70) REVERT: K 121 MET cc_start: 0.9077 (ppp) cc_final: 0.8574 (ppp) REVERT: K 219 GLN cc_start: 0.8043 (pp30) cc_final: 0.7649 (pp30) REVERT: K 221 GLU cc_start: 0.9250 (tp30) cc_final: 0.8292 (tp30) REVERT: K 222 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8473 (pt0) REVERT: K 225 GLN cc_start: 0.9316 (mm-40) cc_final: 0.8952 (mm110) REVERT: K 240 MET cc_start: 0.7067 (ttt) cc_final: 0.6594 (tpp) REVERT: M 67 ASP cc_start: 0.9436 (t0) cc_final: 0.8835 (p0) outliers start: 24 outliers final: 18 residues processed: 268 average time/residue: 0.6164 time to fit residues: 179.6335 Evaluate side-chains 273 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 254 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 85 optimal weight: 40.0000 chunk 63 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 109 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 104 GLN G 73 ASN H 44 GLN H 46 HIS ** K 159 ASN ** 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 = 0.3705 r_free = 0.3705 target = 0.096598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.057081 restraints weight = 129300.344| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.55 r_work: 0.2556 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 95 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 95 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15952 Z= 0.177 Angle : 0.733 19.568 22788 Z= 0.398 Chirality : 0.045 0.218 2606 Planarity : 0.004 0.044 1879 Dihedral : 29.909 128.267 4456 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.15 % Allowed : 23.77 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % 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: 1.20 (0.25), residues: 1136 helix: 1.76 (0.19), residues: 691 sheet: 0.11 (0.49), residues: 118 loop : -1.00 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 112 TYR 0.033 0.002 TYR L 10 PHE 0.019 0.002 PHE M 44 TRP 0.037 0.005 TRP M 76 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 (15952) covalent geometry : angle 0.73324 / 0.40 (22788) hydrogen bonds : bond 0.04081 / 2.69 ( 931) hydrogen bonds : angle 3.48613 / 2.51 ( 2399) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 260 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 31 LYS cc_start: 0.9176 (mmmm) cc_final: 0.8938 (mptt) REVERT: D 90 GLU cc_start: 0.9141 (mp0) cc_final: 0.8638 (mp0) REVERT: E 125 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8749 (mm-40) REVERT: G 94 ASN cc_start: 0.9438 (t0) cc_final: 0.9211 (t160) REVERT: H 31 LYS cc_start: 0.8196 (mppt) cc_final: 0.7956 (mppt) REVERT: H 65 ASP cc_start: 0.9297 (t70) cc_final: 0.9001 (t0) REVERT: K 69 ASN cc_start: 0.9188 (t0) cc_final: 0.8738 (t160) REVERT: K 88 HIS cc_start: 0.9480 (m90) cc_final: 0.8987 (m-70) REVERT: K 111 THR cc_start: 0.9387 (t) cc_final: 0.9177 (t) REVERT: K 121 MET cc_start: 0.9099 (ppp) cc_final: 0.8520 (ppp) REVERT: K 154 ASP cc_start: 0.8183 (t0) cc_final: 0.7782 (t0) REVERT: K 219 GLN cc_start: 0.8079 (pp30) cc_final: 0.7663 (pp30) REVERT: K 221 GLU cc_start: 0.9259 (tp30) cc_final: 0.8324 (tp30) REVERT: K 222 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8480 (pt0) REVERT: K 225 GLN cc_start: 0.9323 (mm-40) cc_final: 0.8966 (mm110) REVERT: K 240 MET cc_start: 0.7052 (ttt) cc_final: 0.6530 (tpp) REVERT: M 67 ASP cc_start: 0.9428 (t0) cc_final: 0.8825 (p0) REVERT: M 83 CYS cc_start: 0.8779 (p) cc_final: 0.8441 (t) outliers start: 21 outliers final: 17 residues processed: 269 average time/residue: 0.6075 time to fit residues: 178.4188 Evaluate side-chains 273 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 27 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 112 optimal weight: 0.0030 chunk 51 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 104 GLN H 44 GLN H 46 HIS ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.097429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.058395 restraints weight = 131405.510| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.56 r_work: 0.2594 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 95 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 95 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15952 Z= 0.145 Angle : 0.725 20.815 22788 Z= 0.394 Chirality : 0.044 0.228 2606 Planarity : 0.004 0.044 1879 Dihedral : 29.764 129.738 4456 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.84 % Allowed : 24.59 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % 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 (0.25), residues: 1136 helix: 1.85 (0.19), residues: 685 sheet: 0.15 (0.49), residues: 118 loop : -0.97 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 112 TYR 0.032 0.002 TYR L 10 PHE 0.017 0.001 PHE M 44 TRP 0.038 0.005 TRP M 76 HIS 0.005 0.001 HIS K 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (15952) covalent geometry : angle 0.72475 / 0.39 (22788) hydrogen bonds : bond 0.03893 / 2.58 ( 931) hydrogen bonds : angle 3.44104 / 2.47 ( 2399) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 265 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.9140 (mtt-85) cc_final: 0.8822 (mtt90) REVERT: C 110 ASN cc_start: 0.9218 (OUTLIER) cc_final: 0.8502 (p0) REVERT: D 31 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8936 (mptt) REVERT: D 90 GLU cc_start: 0.9121 (mp0) cc_final: 0.8637 (mp0) REVERT: H 31 LYS cc_start: 0.8162 (mppt) cc_final: 0.7900 (mppt) REVERT: H 65 ASP cc_start: 0.9290 (t70) cc_final: 0.9009 (t0) REVERT: K 69 ASN cc_start: 0.9143 (t0) cc_final: 0.8659 (t160) REVERT: K 88 HIS cc_start: 0.9456 (m90) cc_final: 0.8959 (m-70) REVERT: K 121 MET cc_start: 0.9113 (ppp) cc_final: 0.8537 (ppp) REVERT: K 219 GLN cc_start: 0.7974 (pp30) cc_final: 0.7508 (pp30) REVERT: K 221 GLU cc_start: 0.9199 (tp30) cc_final: 0.8207 (tp30) REVERT: K 222 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8446 (pt0) REVERT: K 225 GLN cc_start: 0.9307 (mm-40) cc_final: 0.8944 (mm110) REVERT: K 240 MET cc_start: 0.7045 (ttt) cc_final: 0.6543 (tpp) REVERT: M 67 ASP cc_start: 0.9446 (t0) cc_final: 0.9096 (p0) outliers start: 18 outliers final: 14 residues processed: 274 average time/residue: 0.6001 time to fit residues: 179.6341 Evaluate side-chains 277 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 262 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 104 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN C 104 GLN D 106 HIS H 44 GLN H 46 HIS ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.096708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.057777 restraints weight = 109316.740| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.21 r_work: 0.2576 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 95 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 95 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15952 Z= 0.187 Angle : 0.740 19.873 22788 Z= 0.400 Chirality : 0.045 0.221 2606 Planarity : 0.004 0.045 1879 Dihedral : 29.823 130.194 4456 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.54 % Allowed : 25.20 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % 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: 1.25 (0.25), residues: 1136 helix: 1.82 (0.19), residues: 685 sheet: 0.19 (0.50), residues: 118 loop : -1.00 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 112 TYR 0.034 0.002 TYR L 10 PHE 0.016 0.002 PHE E 67 TRP 0.036 0.005 TRP M 76 HIS 0.007 0.001 HIS K 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (15952) covalent geometry : angle 0.74040 / 0.40 (22788) hydrogen bonds : bond 0.04170 / 2.75 ( 931) hydrogen bonds : angle 3.47873 / 2.49 ( 2399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5536.08 seconds wall clock time: 94 minutes 42.25 seconds (5682.25 seconds total)