Starting phenix.real_space_refine on Wed Mar 4 15:20:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oh9_12897/03_2026/7oh9_12897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oh9_12897/03_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_12897/03_2026/7oh9_12897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oh9_12897/03_2026/7oh9_12897.map" model { file = "/net/cci-nas-00/data/ceres_data/7oh9_12897/03_2026/7oh9_12897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oh9_12897/03_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-dev-5986/lib/python3.9/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: 3.98, per 1000 atoms: 0.26 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: 1.35 Conformation dependent library (CDL) restraints added in 497.7 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: 2.39 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: 3.41 Time building geometry restraints manager: 1.81 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=" CB PRO A 38 " pdb=" CG PRO A 38 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.65e+00 bond pdb=" CD GLU L 20 " pdb=" OE1 GLU L 20 " ideal model delta sigma weight residual 1.249 1.211 0.038 1.90e-02 2.77e+03 3.92e+00 bond pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.74e+00 bond pdb=" CB ASN M 55 " pdb=" CG ASN M 55 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.72e+00 bond pdb=" CG1 ILE D 58 " pdb=" CD1 ILE D 58 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.89e+00 ... (remaining 15947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 22510 2.73 - 5.45: 230 5.45 - 8.18: 36 8.18 - 10.90: 10 10.90 - 13.63: 2 Bond angle restraints: 22788 Sorted by residual: 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=" 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 angle pdb=" CA GLU L 20 " pdb=" CB GLU L 20 " pdb=" CG GLU L 20 " ideal model delta sigma weight residual 114.10 123.04 -8.94 2.00e+00 2.50e-01 2.00e+01 angle pdb=" C CYS M 72 " pdb=" N ASP M 73 " pdb=" CA ASP M 73 " ideal model delta sigma weight residual 121.54 129.97 -8.43 1.91e+00 2.74e-01 1.95e+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: 2256 0.069 - 0.139: 314 0.139 - 0.208: 29 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: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.850 Find NCS groups from input model: 0.160 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:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 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= 0.283 Angle : 0.837 13.630 22788 Z= 0.468 Chirality : 0.050 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 covalent geometry : bond 0.00654 (15952) covalent geometry : angle 0.83706 (22788) hydrogen bonds : bond 0.11791 ( 931) hydrogen bonds : angle 4.94666 ( 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 : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash 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 53 SER cc_start: 0.9119 (p) cc_final: 0.8740 (p) REVERT: H 65 ASP cc_start: 0.8494 (t70) cc_final: 0.8242 (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: 0.8325 (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: 0.8705 (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: 0.7291 time to fit residues: 235.5779 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 : 0.427 ------------------------------------------------------------------------------- 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: 7.9990 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: 30.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN 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 Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.095706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.056172 restraints weight = 118538.531| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.36 r_work: 0.2538 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 71 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15952 Z= 0.245 Angle : 0.674 11.267 22788 Z= 0.380 Chirality : 0.041 0.251 2606 Planarity : 0.005 0.051 1879 Dihedral : 29.687 107.653 4458 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.25 % Allowed : 15.06 % Favored : 82.68 % 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: 0.50 (0.24), residues: 1136 helix: 1.08 (0.19), residues: 692 sheet: 0.29 (0.49), residues: 121 loop : -1.19 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 30 TYR 0.054 0.002 TYR L 10 PHE 0.027 0.002 PHE M 44 TRP 0.021 0.002 TRP L 258 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00550 (15952) covalent geometry : angle 0.67428 (22788) hydrogen bonds : bond 0.04252 ( 931) hydrogen bonds : angle 3.63159 ( 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 298 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 276 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9022 (pm20) cc_final: 0.8735 (pm20) REVERT: B 95 ARG cc_start: 0.9198 (mtt-85) cc_final: 0.8946 (mtt90) REVERT: D 31 LYS cc_start: 0.9178 (mmmm) cc_final: 0.8865 (mptt) REVERT: D 90 GLU cc_start: 0.9177 (mp0) cc_final: 0.8945 (mp0) REVERT: E 115 LYS cc_start: 0.9356 (mtmm) cc_final: 0.9107 (mtmm) REVERT: E 120 MET cc_start: 0.9389 (OUTLIER) cc_final: 0.8892 (mtm) REVERT: H 65 ASP cc_start: 0.9245 (t70) cc_final: 0.8914 (t0) REVERT: K 88 HIS cc_start: 0.9501 (m-70) cc_final: 0.8949 (m-70) REVERT: K 91 ASN cc_start: 0.8819 (m-40) cc_final: 0.8422 (m-40) REVERT: K 121 MET cc_start: 0.8852 (ppp) cc_final: 0.8531 (ppp) REVERT: K 139 TYR cc_start: 0.8759 (m-80) cc_final: 0.7567 (m-80) REVERT: K 144 GLN cc_start: 0.8992 (mt0) cc_final: 0.8708 (mm110) REVERT: K 221 GLU cc_start: 0.9146 (tp30) cc_final: 0.8767 (tp30) REVERT: K 224 TYR cc_start: 0.9495 (m-10) cc_final: 0.9259 (m-10) REVERT: L 248 TYR cc_start: 0.9175 (p90) cc_final: 0.8444 (p90) REVERT: M 83 CYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8492 (t) REVERT: M 112 ARG cc_start: 0.8819 (tmm-80) cc_final: 0.8570 (tmm-80) outliers start: 22 outliers final: 10 residues processed: 282 average time/residue: 0.6899 time to fit residues: 210.7356 Evaluate side-chains 269 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 257 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 120 MET 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 K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 83 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 62 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 104 GLN G 94 ASN H 44 GLN H 46 HIS ** K 68 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 = 0.3720 r_free = 0.3720 target = 0.097478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.058542 restraints weight = 134200.765| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.62 r_work: 0.2586 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 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 = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.2591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15952 Z= 0.164 Angle : 0.644 13.147 22788 Z= 0.363 Chirality : 0.038 0.180 2606 Planarity : 0.004 0.047 1879 Dihedral : 29.274 108.903 4456 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.07 % Allowed : 17.83 % 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: 1.07 (0.24), residues: 1136 helix: 1.55 (0.19), residues: 691 sheet: 0.47 (0.48), residues: 127 loop : -1.02 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 30 TYR 0.045 0.002 TYR L 10 PHE 0.024 0.001 PHE M 44 TRP 0.023 0.003 TRP M 76 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00359 (15952) covalent geometry : angle 0.64358 (22788) hydrogen bonds : bond 0.03686 ( 931) hydrogen bonds : angle 3.39422 ( 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 305 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 275 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 GLN cc_start: 0.8968 (mt0) cc_final: 0.8765 (mt0) REVERT: D 31 LYS cc_start: 0.9179 (mmmm) cc_final: 0.8931 (mptt) REVERT: D 90 GLU cc_start: 0.9160 (mp0) cc_final: 0.8694 (mp0) REVERT: E 120 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.8954 (mtm) REVERT: H 65 ASP cc_start: 0.9267 (t70) cc_final: 0.8941 (t0) REVERT: K 69 ASN cc_start: 0.9307 (t0) cc_final: 0.8733 (t160) REVERT: K 88 HIS cc_start: 0.9549 (m-70) cc_final: 0.8986 (m-70) REVERT: K 111 THR cc_start: 0.9455 (t) cc_final: 0.9226 (t) REVERT: K 121 MET cc_start: 0.8909 (ppp) cc_final: 0.8497 (ppp) REVERT: K 144 GLN cc_start: 0.9015 (mt0) cc_final: 0.8773 (mm110) REVERT: K 221 GLU cc_start: 0.9177 (tp30) cc_final: 0.8641 (tp30) REVERT: K 224 TYR cc_start: 0.9554 (m-10) cc_final: 0.9155 (m-10) REVERT: K 225 GLN cc_start: 0.9328 (mm-40) cc_final: 0.8988 (mm110) REVERT: L 20 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: L 248 TYR cc_start: 0.9153 (p90) cc_final: 0.8215 (p90) REVERT: M 71 PHE cc_start: 0.8203 (t80) cc_final: 0.7691 (t80) REVERT: M 112 ARG cc_start: 0.8741 (tmm-80) cc_final: 0.8481 (tmm-80) outliers start: 30 outliers final: 11 residues processed: 282 average time/residue: 0.6949 time to fit residues: 212.1618 Evaluate side-chains 272 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 259 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER 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 E residue 120 MET 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 20 GLU Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 85 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: 6.9990 chunk 16 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 24 GLN C 38 ASN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 46 HIS K 88 HIS ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.094014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.054457 restraints weight = 107553.452| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.20 r_work: 0.2492 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2493 r_free = 0.2493 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2493 r_free = 0.2493 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.2493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 15952 Z= 0.348 Angle : 0.705 13.213 22788 Z= 0.396 Chirality : 0.043 0.167 2606 Planarity : 0.005 0.044 1879 Dihedral : 29.911 111.519 4456 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.48 % Allowed : 18.44 % Favored : 78.07 % 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: 1.06 (0.24), residues: 1136 helix: 1.54 (0.19), residues: 691 sheet: 0.38 (0.48), residues: 127 loop : -0.98 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 30 TYR 0.045 0.002 TYR L 10 PHE 0.018 0.002 PHE M 44 TRP 0.022 0.002 TRP L 258 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00791 (15952) covalent geometry : angle 0.70501 (22788) hydrogen bonds : bond 0.04555 ( 931) hydrogen bonds : angle 3.58714 ( 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 295 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9003 (m-30) cc_final: 0.8780 (m-30) REVERT: D 30 ARG cc_start: 0.8521 (mpt-90) cc_final: 0.8177 (mtt-85) REVERT: D 31 LYS cc_start: 0.9172 (mmmm) cc_final: 0.8898 (mptt) REVERT: D 90 GLU cc_start: 0.9207 (mp0) cc_final: 0.8699 (mp0) REVERT: E 120 MET cc_start: 0.9402 (OUTLIER) cc_final: 0.9120 (mtp) REVERT: E 125 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: H 65 ASP cc_start: 0.9281 (t70) cc_final: 0.8950 (t0) REVERT: K 69 ASN cc_start: 0.9281 (t0) cc_final: 0.8763 (t160) REVERT: K 88 HIS cc_start: 0.9444 (m90) cc_final: 0.8955 (m-70) REVERT: K 93 GLU cc_start: 0.7407 (mp0) cc_final: 0.7112 (mp0) REVERT: K 121 MET cc_start: 0.8922 (ppp) cc_final: 0.8465 (ppp) REVERT: K 144 GLN cc_start: 0.9016 (mt0) cc_final: 0.8750 (mm110) REVERT: K 221 GLU cc_start: 0.9214 (tp30) cc_final: 0.8614 (tp30) REVERT: K 224 TYR cc_start: 0.9558 (m-10) cc_final: 0.9083 (m-10) REVERT: K 225 GLN cc_start: 0.9345 (mm-40) cc_final: 0.8992 (mm110) REVERT: M 76 TRP cc_start: 0.8790 (m100) cc_final: 0.8586 (m100) outliers start: 34 outliers final: 16 residues processed: 274 average time/residue: 0.7117 time to fit residues: 210.7278 Evaluate side-chains 257 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 239 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 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 120 MET Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 62 ILE 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 54 LYS 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 113 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 46 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 104 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.096690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.057747 restraints weight = 107317.913| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.20 r_work: 0.2582 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- 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: 80 | |-----------------------------------------------------------------------------| |-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: 86 | |-----------------------------------------------------------------------------| r_final: 0.2582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15952 Z= 0.177 Angle : 0.663 14.214 22788 Z= 0.370 Chirality : 0.038 0.180 2606 Planarity : 0.004 0.045 1879 Dihedral : 29.381 115.222 4456 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.46 % Allowed : 21.72 % Favored : 75.82 % 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: 1.35 (0.25), residues: 1136 helix: 1.78 (0.19), residues: 691 sheet: 0.40 (0.48), residues: 127 loop : -0.84 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.037 0.002 TYR L 10 PHE 0.017 0.001 PHE M 78 TRP 0.024 0.002 TRP L 258 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00393 (15952) covalent geometry : angle 0.66326 (22788) hydrogen bonds : bond 0.03636 ( 931) hydrogen bonds : angle 3.40914 ( 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 298 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 274 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 110 ASN cc_start: 0.9261 (OUTLIER) cc_final: 0.8630 (p0) REVERT: D 30 ARG cc_start: 0.8481 (mpt-90) cc_final: 0.8130 (mtt-85) REVERT: D 31 LYS cc_start: 0.9156 (mmmm) cc_final: 0.8914 (mptt) REVERT: D 90 GLU cc_start: 0.9139 (mp0) cc_final: 0.8601 (mp0) REVERT: E 120 MET cc_start: 0.9406 (OUTLIER) cc_final: 0.9116 (mtp) REVERT: G 94 ASN cc_start: 0.9428 (t0) cc_final: 0.9156 (t160) REVERT: H 31 LYS cc_start: 0.8261 (mppt) cc_final: 0.7905 (mptt) REVERT: H 65 ASP cc_start: 0.9274 (t70) cc_final: 0.8985 (t0) REVERT: H 76 ARG cc_start: 0.8794 (mtm110) cc_final: 0.8520 (mtm110) REVERT: K 69 ASN cc_start: 0.9262 (t0) cc_final: 0.8793 (t160) REVERT: K 88 HIS cc_start: 0.9438 (m90) cc_final: 0.9091 (m90) REVERT: K 121 MET cc_start: 0.8924 (ppp) cc_final: 0.8518 (ppp) REVERT: K 219 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7951 (pp30) REVERT: K 221 GLU cc_start: 0.9159 (tp30) cc_final: 0.8524 (tp30) REVERT: K 222 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8575 (pt0) REVERT: K 224 TYR cc_start: 0.9586 (m-10) cc_final: 0.9156 (m-10) REVERT: K 225 GLN cc_start: 0.9332 (mm-40) cc_final: 0.9001 (mm110) REVERT: L 20 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7003 (pm20) REVERT: M 67 ASP cc_start: 0.9467 (t0) cc_final: 0.8936 (p0) REVERT: M 76 TRP cc_start: 0.8820 (m100) cc_final: 0.8447 (m100) outliers start: 24 outliers final: 16 residues processed: 283 average time/residue: 0.6738 time to fit residues: 206.8163 Evaluate side-chains 279 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 260 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER 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 E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU 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 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 214 LEU Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 92 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 135 optimal weight: 30.0000 chunk 133 optimal weight: 30.0000 chunk 108 optimal weight: 0.3980 chunk 118 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 104 GLN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.096885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.057586 restraints weight = 129020.174| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.56 r_work: 0.2569 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15952 Z= 0.183 Angle : 0.675 18.029 22788 Z= 0.374 Chirality : 0.038 0.274 2606 Planarity : 0.004 0.045 1879 Dihedral : 29.353 114.342 4456 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.77 % Allowed : 22.23 % Favored : 75.00 % 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: 1.40 (0.25), residues: 1136 helix: 1.81 (0.19), residues: 691 sheet: 0.29 (0.48), residues: 127 loop : -0.72 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.035 0.002 TYR L 10 PHE 0.020 0.001 PHE M 44 TRP 0.024 0.002 TRP L 258 HIS 0.004 0.001 HIS K 179 Details of bonding type rmsd covalent geometry : bond 0.00412 (15952) covalent geometry : angle 0.67492 (22788) hydrogen bonds : bond 0.03669 ( 931) hydrogen bonds : angle 3.37240 ( 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 297 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 270 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 110 ASN cc_start: 0.9267 (OUTLIER) cc_final: 0.8696 (p0) REVERT: D 30 ARG cc_start: 0.8468 (mpt-90) cc_final: 0.8157 (mtt-85) REVERT: D 31 LYS cc_start: 0.9169 (mmmm) cc_final: 0.8899 (mptt) REVERT: D 54 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8835 (mmmm) REVERT: D 90 GLU cc_start: 0.9148 (mp0) cc_final: 0.8584 (mp0) REVERT: E 120 MET cc_start: 0.9428 (OUTLIER) cc_final: 0.9151 (mtp) REVERT: G 94 ASN cc_start: 0.9442 (t0) cc_final: 0.9172 (t160) REVERT: H 31 LYS cc_start: 0.8238 (mppt) cc_final: 0.7854 (mptt) REVERT: H 65 ASP cc_start: 0.9304 (t70) cc_final: 0.9021 (t0) REVERT: K 69 ASN cc_start: 0.9244 (t0) cc_final: 0.8257 (m-40) REVERT: K 75 THR cc_start: 0.9174 (m) cc_final: 0.8932 (p) REVERT: K 88 HIS cc_start: 0.9463 (m90) cc_final: 0.8956 (m-70) REVERT: K 111 THR cc_start: 0.9369 (t) cc_final: 0.9149 (t) REVERT: K 121 MET cc_start: 0.8981 (ppp) cc_final: 0.8481 (ppp) REVERT: K 154 ASP cc_start: 0.8493 (t0) cc_final: 0.8151 (t0) REVERT: K 158 GLN cc_start: 0.9292 (mm110) cc_final: 0.8962 (mp10) REVERT: K 221 GLU cc_start: 0.9192 (tp30) cc_final: 0.8519 (tp30) REVERT: K 224 TYR cc_start: 0.9583 (m-10) cc_final: 0.9167 (m-10) REVERT: K 225 GLN cc_start: 0.9348 (mm-40) cc_final: 0.8987 (mm110) REVERT: K 240 MET cc_start: 0.7062 (ttt) cc_final: 0.6528 (tpp) REVERT: L 20 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8010 (pm20) REVERT: M 67 ASP cc_start: 0.9330 (t0) cc_final: 0.8919 (p0) REVERT: M 76 TRP cc_start: 0.8803 (m100) cc_final: 0.8535 (m100) outliers start: 27 outliers final: 19 residues processed: 282 average time/residue: 0.6767 time to fit residues: 206.7429 Evaluate side-chains 282 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR 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 120 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 111 ILE 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 K residue 214 LEU Chi-restraints excluded: chain L residue 20 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 114 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 135 optimal weight: 50.0000 chunk 115 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 38 ASN G 73 ASN H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 HIS ** 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 = 0.3684 r_free = 0.3684 target = 0.095024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.055505 restraints weight = 122360.915| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.35 r_work: 0.2526 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15952 Z= 0.285 Angle : 0.708 18.570 22788 Z= 0.392 Chirality : 0.041 0.178 2606 Planarity : 0.004 0.043 1879 Dihedral : 29.666 113.920 4456 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.66 % Allowed : 23.87 % Favored : 73.46 % 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: 1.27 (0.25), residues: 1136 helix: 1.68 (0.19), residues: 691 sheet: 0.40 (0.47), residues: 131 loop : -0.79 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.036 0.002 TYR L 10 PHE 0.021 0.002 PHE M 44 TRP 0.022 0.002 TRP L 258 HIS 0.005 0.001 HIS K 179 Details of bonding type rmsd covalent geometry : bond 0.00648 (15952) covalent geometry : angle 0.70799 (22788) hydrogen bonds : bond 0.04191 ( 931) hydrogen bonds : angle 3.49579 ( 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 285 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 259 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.9307 (mtp85) cc_final: 0.9045 (mtp85) REVERT: C 110 ASN cc_start: 0.9324 (OUTLIER) cc_final: 0.8681 (p0) REVERT: D 30 ARG cc_start: 0.8478 (mpt-90) cc_final: 0.8158 (mtt-85) REVERT: D 31 LYS cc_start: 0.9124 (mmmm) cc_final: 0.8896 (mptt) REVERT: D 90 GLU cc_start: 0.9196 (mp0) cc_final: 0.8693 (mp0) REVERT: E 120 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.9115 (mtp) REVERT: E 125 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8745 (mm-40) REVERT: H 65 ASP cc_start: 0.9260 (t70) cc_final: 0.8928 (t0) REVERT: K 69 ASN cc_start: 0.9227 (t0) cc_final: 0.8276 (m-40) REVERT: K 75 THR cc_start: 0.9206 (m) cc_final: 0.8962 (p) REVERT: K 88 HIS cc_start: 0.9467 (m90) cc_final: 0.9202 (m90) REVERT: K 121 MET cc_start: 0.9021 (ppp) cc_final: 0.8484 (ppp) REVERT: K 144 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8685 (mm-40) REVERT: K 154 ASP cc_start: 0.8618 (t0) cc_final: 0.8316 (t0) REVERT: K 221 GLU cc_start: 0.9172 (tp30) cc_final: 0.8545 (tp30) REVERT: K 224 TYR cc_start: 0.9583 (m-10) cc_final: 0.9107 (m-10) REVERT: K 225 GLN cc_start: 0.9316 (mm-40) cc_final: 0.8959 (mm110) REVERT: K 240 MET cc_start: 0.7224 (ttt) cc_final: 0.6712 (tpp) REVERT: L 20 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: M 76 TRP cc_start: 0.8887 (m100) cc_final: 0.8623 (m100) REVERT: M 78 PHE cc_start: 0.9240 (m-80) cc_final: 0.9027 (m-80) REVERT: M 108 VAL cc_start: 0.8054 (t) cc_final: 0.7433 (p) outliers start: 26 outliers final: 19 residues processed: 272 average time/residue: 0.6831 time to fit residues: 200.9626 Evaluate side-chains 272 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 249 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER 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 57 SER Chi-restraints excluded: chain E residue 120 MET 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 54 LYS Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain L residue 40 ASN Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 85 VAL 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: 2.9990 chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** K 68 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 = 0.3726 r_free = 0.3726 target = 0.097324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.058236 restraints weight = 138661.457| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.58 r_work: 0.2594 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15952 Z= 0.166 Angle : 0.691 21.445 22788 Z= 0.378 Chirality : 0.038 0.183 2606 Planarity : 0.004 0.044 1879 Dihedral : 29.302 115.596 4456 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.36 % Allowed : 24.80 % Favored : 72.85 % 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: 1.41 (0.25), residues: 1136 helix: 1.82 (0.19), residues: 691 sheet: 0.27 (0.47), residues: 130 loop : -0.73 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.032 0.002 TYR L 10 PHE 0.022 0.001 PHE M 44 TRP 0.019 0.002 TRP L 258 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00369 (15952) covalent geometry : angle 0.69096 (22788) hydrogen bonds : bond 0.03631 ( 931) hydrogen bonds : angle 3.40142 ( 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 288 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 265 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 110 ASN cc_start: 0.9271 (OUTLIER) cc_final: 0.8710 (p0) REVERT: D 30 ARG cc_start: 0.8437 (mpt-90) cc_final: 0.8131 (mtt-85) REVERT: D 31 LYS cc_start: 0.9131 (mmmm) cc_final: 0.8915 (mptt) REVERT: D 90 GLU cc_start: 0.9155 (mp0) cc_final: 0.8581 (mp0) REVERT: E 120 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.9090 (mtp) REVERT: E 125 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8645 (mm-40) REVERT: H 31 LYS cc_start: 0.8246 (mppt) cc_final: 0.7836 (mptt) REVERT: H 65 ASP cc_start: 0.9265 (t70) cc_final: 0.8981 (t0) REVERT: H 76 ARG cc_start: 0.8838 (mtm110) cc_final: 0.8508 (mtm110) REVERT: K 69 ASN cc_start: 0.9206 (t0) cc_final: 0.8237 (m-40) REVERT: K 75 THR cc_start: 0.9212 (m) cc_final: 0.8963 (p) REVERT: K 88 HIS cc_start: 0.9462 (m90) cc_final: 0.9201 (m90) REVERT: K 121 MET cc_start: 0.8929 (ppp) cc_final: 0.8324 (ppp) REVERT: K 154 ASP cc_start: 0.8601 (t0) cc_final: 0.8298 (t0) REVERT: K 219 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7965 (pp30) REVERT: K 221 GLU cc_start: 0.9131 (tp30) cc_final: 0.8430 (tp30) REVERT: K 224 TYR cc_start: 0.9579 (m-10) cc_final: 0.9134 (m-10) REVERT: K 225 GLN cc_start: 0.9318 (mm-40) cc_final: 0.8985 (mm110) REVERT: K 240 MET cc_start: 0.7043 (ttt) cc_final: 0.6550 (tpp) REVERT: L 20 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7895 (pm20) outliers start: 23 outliers final: 15 residues processed: 279 average time/residue: 0.6737 time to fit residues: 203.4133 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 : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER 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 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 120 MET 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 K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain M residue 42 GLU 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: 10.0000 chunk 63 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.096350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.057147 restraints weight = 128856.477| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.43 r_work: 0.2566 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 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 = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15952 Z= 0.222 Angle : 0.714 21.020 22788 Z= 0.389 Chirality : 0.039 0.179 2606 Planarity : 0.004 0.043 1879 Dihedral : 29.421 114.836 4456 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.46 % Allowed : 25.51 % Favored : 72.03 % 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: 1.33 (0.25), residues: 1136 helix: 1.78 (0.19), residues: 691 sheet: 0.30 (0.47), residues: 131 loop : -0.83 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.034 0.002 TYR L 10 PHE 0.022 0.002 PHE M 44 TRP 0.031 0.004 TRP M 76 HIS 0.004 0.001 HIS K 179 Details of bonding type rmsd covalent geometry : bond 0.00504 (15952) covalent geometry : angle 0.71418 (22788) hydrogen bonds : bond 0.03806 ( 931) hydrogen bonds : angle 3.45226 ( 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 276 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 110 ASN cc_start: 0.9307 (OUTLIER) cc_final: 0.8710 (p0) REVERT: D 27 ARG cc_start: 0.5939 (OUTLIER) cc_final: 0.5720 (tpm-80) REVERT: D 30 ARG cc_start: 0.8334 (mpt-90) cc_final: 0.7985 (mtt-85) REVERT: D 31 LYS cc_start: 0.9125 (mmmm) cc_final: 0.8880 (mptt) REVERT: D 90 GLU cc_start: 0.9172 (mp0) cc_final: 0.8574 (mp0) REVERT: E 120 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.9101 (mtp) REVERT: H 31 LYS cc_start: 0.8289 (mppt) cc_final: 0.7865 (mptt) REVERT: H 65 ASP cc_start: 0.9259 (t70) cc_final: 0.8956 (t0) REVERT: H 76 ARG cc_start: 0.8835 (mtm110) cc_final: 0.8528 (mtm110) REVERT: K 69 ASN cc_start: 0.9128 (t0) cc_final: 0.8338 (m-40) REVERT: K 75 THR cc_start: 0.9205 (m) cc_final: 0.8954 (p) REVERT: K 88 HIS cc_start: 0.9449 (m90) cc_final: 0.9192 (m90) REVERT: K 121 MET cc_start: 0.9005 (ppp) cc_final: 0.8442 (ppp) REVERT: K 154 ASP cc_start: 0.8619 (t0) cc_final: 0.8306 (t0) REVERT: K 221 GLU cc_start: 0.9135 (tp30) cc_final: 0.8548 (tp30) REVERT: K 224 TYR cc_start: 0.9590 (m-10) cc_final: 0.9145 (m-10) REVERT: K 225 GLN cc_start: 0.9323 (mm-40) cc_final: 0.9003 (mm110) REVERT: K 240 MET cc_start: 0.7213 (ttt) cc_final: 0.6709 (tpp) REVERT: L 20 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: M 108 VAL cc_start: 0.7977 (t) cc_final: 0.7393 (p) outliers start: 24 outliers final: 16 residues processed: 264 average time/residue: 0.6806 time to fit residues: 194.3936 Evaluate side-chains 269 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 249 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 81 ASP 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 27 ARG Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 62 ILE 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 K residue 214 LEU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain M residue 42 GLU 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: 9.9990 chunk 111 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 112 optimal weight: 0.0060 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN D 106 HIS G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** K 68 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 = 0.3729 r_free = 0.3729 target = 0.097525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.058625 restraints weight = 130804.518| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.49 r_work: 0.2606 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 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 = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 95 | |-----------------------------------------------------------------------------| r_final: 0.2613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15952 Z= 0.171 Angle : 0.718 21.766 22788 Z= 0.389 Chirality : 0.038 0.184 2606 Planarity : 0.004 0.043 1879 Dihedral : 29.286 115.562 4456 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.74 % Allowed : 26.13 % Favored : 72.13 % 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: 1.38 (0.25), residues: 1136 helix: 1.86 (0.19), residues: 690 sheet: 0.44 (0.48), residues: 121 loop : -0.96 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.032 0.002 TYR L 10 PHE 0.018 0.001 PHE M 44 TRP 0.038 0.004 TRP M 76 HIS 0.006 0.001 HIS K 179 Details of bonding type rmsd covalent geometry : bond 0.00382 (15952) covalent geometry : angle 0.71772 (22788) hydrogen bonds : bond 0.03562 ( 931) hydrogen bonds : angle 3.40411 ( 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 273 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 256 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: C 110 ASN cc_start: 0.9293 (OUTLIER) cc_final: 0.8726 (p0) REVERT: D 30 ARG cc_start: 0.8335 (mpt-90) cc_final: 0.8037 (mtt-85) REVERT: D 31 LYS cc_start: 0.9131 (mmmm) cc_final: 0.8895 (mptt) REVERT: D 90 GLU cc_start: 0.9151 (mp0) cc_final: 0.8578 (mp0) REVERT: D 105 LYS cc_start: 0.8974 (ptpp) cc_final: 0.8687 (pttm) REVERT: E 120 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.9140 (mtp) REVERT: G 72 ASP cc_start: 0.8833 (m-30) cc_final: 0.8566 (m-30) REVERT: H 31 LYS cc_start: 0.8305 (mppt) cc_final: 0.7875 (mptt) REVERT: H 65 ASP cc_start: 0.9253 (t70) cc_final: 0.8979 (t0) REVERT: H 76 ARG cc_start: 0.8843 (mtm110) cc_final: 0.8531 (mtm110) REVERT: K 69 ASN cc_start: 0.9094 (t0) cc_final: 0.8337 (m-40) REVERT: K 75 THR cc_start: 0.9175 (m) cc_final: 0.8936 (p) REVERT: K 88 HIS cc_start: 0.9435 (m90) cc_final: 0.9178 (m90) REVERT: K 98 ARG cc_start: 0.8868 (tpt90) cc_final: 0.8628 (mmm160) REVERT: K 121 MET cc_start: 0.8980 (ppp) cc_final: 0.8361 (ppp) REVERT: K 144 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8547 (mm-40) REVERT: K 154 ASP cc_start: 0.8630 (t0) cc_final: 0.8310 (t0) REVERT: K 195 TYR cc_start: 0.9029 (t80) cc_final: 0.8737 (t80) REVERT: K 221 GLU cc_start: 0.9217 (tp30) cc_final: 0.8652 (tp30) REVERT: K 224 TYR cc_start: 0.9568 (m-10) cc_final: 0.9166 (m-10) REVERT: K 225 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8997 (mm110) REVERT: K 240 MET cc_start: 0.7110 (ttt) cc_final: 0.6642 (tpp) outliers start: 17 outliers final: 13 residues processed: 265 average time/residue: 0.6857 time to fit residues: 196.8935 Evaluate side-chains 269 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER 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 57 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 30.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 73 ASN H 44 GLN ** K 68 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 = 0.3694 r_free = 0.3694 target = 0.095706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.056501 restraints weight = 108640.690| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.19 r_work: 0.2559 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 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 = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 95 | |-----------------------------------------------------------------------------| r_final: 0.2566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15952 Z= 0.266 Angle : 0.739 20.017 22788 Z= 0.403 Chirality : 0.041 0.184 2606 Planarity : 0.004 0.043 1879 Dihedral : 29.473 113.867 4456 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.84 % Allowed : 26.23 % Favored : 71.93 % 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: 1.22 (0.25), residues: 1136 helix: 1.75 (0.19), residues: 690 sheet: 0.10 (0.47), residues: 131 loop : -0.94 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 92 TYR 0.035 0.002 TYR L 10 PHE 0.018 0.002 PHE M 78 TRP 0.039 0.004 TRP M 76 HIS 0.007 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00605 (15952) covalent geometry : angle 0.73922 (22788) hydrogen bonds : bond 0.04154 ( 931) hydrogen bonds : angle 3.49124 ( 2399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6093.90 seconds wall clock time: 104 minutes 1.81 seconds (6241.81 seconds total)