Starting phenix.real_space_refine on Sat Sep 12 04:33:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oha_12898/09_2026/7oha_12898.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oha_12898/09_2026/7oha_12898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7oha_12898/09_2026/7oha_12898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oha_12898/09_2026/7oha_12898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oha_12898/09_2026/7oha_12898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oha_12898/09_2026/7oha_12898.map" } resolution = 2.9 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 244 5.49 5 S 25 5.16 5 C 8189 2.51 5 N 2623 2.21 5 O 3134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14215 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: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2483 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "J" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2519 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "K" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Chain: "L" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 884 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 106} Chain breaks: 1 Chain: "M" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Link IDs: {'TRANS': 106} Chain breaks: 1 Time building chain proxies: 2.77, per 1000 atoms: 0.19 Number of scatterers: 14215 At special positions: 0 Unit cell: (113.4, 114.45, 130.2, 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 244 15.00 O 3134 8.00 N 2623 7.00 C 8189 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: 1.12 Conformation dependent library (CDL) restraints added in 538.3 milliseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2182 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 11 sheets defined 60.5% alpha, 13.2% beta 122 base pairs and 231 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.785A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.553A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.545A 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 removed outlier: 3.523A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.868A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.320A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.514A 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 '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 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.540A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.610A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 29 removed outlier: 3.922A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (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 92 removed outlier: 3.519A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) 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: 4.292A 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 'G' and resid 112 through 116 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: 3.715A pdb=" N VAL K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 147 removed outlier: 3.584A pdb=" N GLY K 147 " --> pdb=" O ILE K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 179 removed outlier: 3.783A pdb=" N LEU K 175 " --> pdb=" O ARG K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 219 through 237 removed outlier: 3.829A 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 28 removed outlier: 3.716A pdb=" N ARG L 22 " --> pdb=" O VAL L 18 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU L 23 " --> pdb=" O ASN L 19 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE L 25 " --> pdb=" O VAL L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 49 removed outlier: 3.604A pdb=" N GLN L 36 " --> pdb=" O GLU L 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 12 removed outlier: 3.568A pdb=" N ARG M 11 " --> pdb=" O GLU M 8 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG M 12 " --> pdb=" O LEU M 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 8 through 12' Processing helix chain 'M' and resid 13 through 30 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: 6.983A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.343A 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: 7.076A 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: 7.539A 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 193 through 195 removed outlier: 4.040A pdb=" N GLY K 216 " --> pdb=" O ILE K 160 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE K 160 " --> pdb=" O GLY K 216 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE K 155 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N THR K 75 " --> pdb=" O PHE K 155 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE K 157 " --> pdb=" O THR K 73 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR K 73 " --> pdb=" O ILE K 157 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN K 69 " --> pdb=" O VAL K 161 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER K 163 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU K 67 " --> pdb=" O SER K 163 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE K 70 " --> pdb=" O GLY K 125 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY K 125 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR K 111 " --> pdb=" O ILE K 106 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE K 106 " --> pdb=" O THR K 111 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA K 92 " --> pdb=" O PHE M 71 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LYS M 59 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL M 87 " --> pdb=" O LYS M 59 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR M 61 " --> pdb=" O VAL M 85 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL M 85 " --> pdb=" O THR M 61 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS M 63 " --> pdb=" O CYS M 83 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N CYS M 83 " --> pdb=" O LYS M 63 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE M 79 " --> pdb=" O ASP M 67 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR M 69 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR M 77 " --> pdb=" O TYR M 69 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE M 71 " --> pdb=" O VAL M 75 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL M 75 " --> pdb=" O PHE M 71 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP M 109 " --> pdb=" O ASN M 82 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLN M 84 " --> pdb=" O SER M 107 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N SER M 107 " --> pdb=" O GLN M 84 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR M 86 " --> pdb=" O VAL M 105 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL M 105 " --> pdb=" O THR M 86 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU M 88 " --> pdb=" O GLN M 103 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN M 103 " --> pdb=" O GLU M 88 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N MET L 244 " --> pdb=" O VAL M 114 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N CYS M 116 " --> pdb=" O MET L 244 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N CYS L 246 " --> pdb=" O CYS M 116 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU L 243 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL L 267 " --> pdb=" O LEU L 243 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU L 245 " --> pdb=" O GLY L 265 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY L 265 " --> pdb=" O LEU L 245 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N SER L 261 " --> pdb=" O ASP L 249 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN L 277 " --> pdb=" O ASP L 264 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL L 266 " --> pdb=" O THR L 275 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR L 275 " --> pdb=" O VAL L 266 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR L 268 " --> pdb=" O ASP L 273 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASP L 273 " --> pdb=" O THR L 268 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N LEU M 60 " --> pdb=" O PHE L 276 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LYS L 278 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N VAL M 62 " --> pdb=" O LYS L 278 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN L 280 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLY M 64 " --> pdb=" O GLN L 280 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLU L 282 " --> pdb=" O GLY M 64 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU M 66 " --> pdb=" O GLU L 282 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU L 284 " --> pdb=" O LEU M 66 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N THR M 68 " --> pdb=" O GLU L 284 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1641 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 316 hydrogen bonds 632 hydrogen bond angles 0 basepair planarities 122 basepair parallelities 231 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1899 1.32 - 1.45: 5114 1.45 - 1.57: 7408 1.57 - 1.70: 487 1.70 - 1.82: 41 Bond restraints: 14949 Sorted by residual: bond pdb=" C5' DT I -26 " pdb=" C4' DT I -26 " ideal model delta sigma weight residual 1.512 1.537 -0.025 7.00e-03 2.04e+04 1.26e+01 bond pdb=" C3' DG J 20 " pdb=" C2' DG J 20 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DC I 21 " pdb=" C2' DC I 21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DG J -10 " pdb=" C2' DG J -10 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DA I 29 " pdb=" C2' DA I 29 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 ... (remaining 14944 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 21022 3.50 - 6.99: 175 6.99 - 10.49: 15 10.49 - 13.98: 4 13.98 - 17.48: 3 Bond angle restraints: 21219 Sorted by residual: angle pdb=" N GLN K 225 " pdb=" CA GLN K 225 " pdb=" CB GLN K 225 " ideal model delta sigma weight residual 110.16 120.89 -10.73 1.48e+00 4.57e-01 5.26e+01 angle pdb=" O4' DG I -24 " pdb=" C1' DG I -24 " pdb=" N9 DG I -24 " ideal model delta sigma weight residual 108.00 103.85 4.15 7.00e-01 2.04e+00 3.51e+01 angle pdb=" CA LYS M 63 " pdb=" CB LYS M 63 " pdb=" CG LYS M 63 " ideal model delta sigma weight residual 114.10 125.19 -11.09 2.00e+00 2.50e-01 3.07e+01 angle pdb=" CA GLN K 225 " pdb=" CB GLN K 225 " pdb=" CG GLN K 225 " ideal model delta sigma weight residual 114.10 124.22 -10.12 2.00e+00 2.50e-01 2.56e+01 angle pdb=" CA LEU L 46 " pdb=" CB LEU L 46 " pdb=" CG LEU L 46 " ideal model delta sigma weight residual 116.30 133.78 -17.48 3.50e+00 8.16e-02 2.49e+01 ... (remaining 21214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.54: 6093 19.54 - 39.08: 1093 39.08 - 58.61: 1129 58.61 - 78.15: 91 78.15 - 97.69: 3 Dihedral angle restraints: 8409 sinusoidal: 5037 harmonic: 3372 Sorted by residual: dihedral pdb=" N GLN K 225 " pdb=" C GLN K 225 " pdb=" CA GLN K 225 " pdb=" CB GLN K 225 " ideal model delta harmonic sigma weight residual 122.80 133.34 -10.54 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CA ASP A 81 " pdb=" CB ASP A 81 " ideal model delta harmonic sigma weight residual 122.80 132.08 -9.28 0 2.50e+00 1.60e-01 1.38e+01 dihedral pdb=" N ASN M 82 " pdb=" C ASN M 82 " pdb=" CA ASN M 82 " pdb=" CB ASN M 82 " ideal model delta harmonic sigma weight residual 122.80 131.84 -9.04 0 2.50e+00 1.60e-01 1.31e+01 ... (remaining 8406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2294 0.108 - 0.216: 119 0.216 - 0.324: 11 0.324 - 0.432: 1 0.432 - 0.540: 2 Chirality restraints: 2427 Sorted by residual: chirality pdb=" CB ILE K 223 " pdb=" CA ILE K 223 " pdb=" CG1 ILE K 223 " pdb=" CG2 ILE K 223 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.54 2.00e-01 2.50e+01 7.29e+00 chirality pdb=" CG LEU M 23 " pdb=" CB LEU M 23 " pdb=" CD1 LEU M 23 " pdb=" CD2 LEU M 23 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.44e+00 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 -2.22 -0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 2424 not shown) Planarity restraints: 1841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 81 " 0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" CG ASP A 81 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASP A 81 " 0.027 2.00e-02 2.50e+03 pdb=" OD2 ASP A 81 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS M 81 " -0.018 2.00e-02 2.50e+03 3.80e-02 1.45e+01 pdb=" C LYS M 81 " 0.066 2.00e-02 2.50e+03 pdb=" O LYS M 81 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN M 82 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU K 186 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO K 187 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO K 187 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO K 187 " 0.042 5.00e-02 4.00e+02 ... (remaining 1838 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2468 2.78 - 3.31: 12602 3.31 - 3.84: 27869 3.84 - 4.37: 32951 4.37 - 4.90: 47954 Nonbonded interactions: 123844 Sorted by model distance: nonbonded pdb=" O THR L 275 " pdb=" OG SER M 58 " model vdw 2.248 3.040 nonbonded pdb=" OG SER K 183 " pdb=" O ILE K 194 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR M 7 " pdb=" O ASN M 117 " model vdw 2.296 3.040 nonbonded pdb=" NH1 ARG G 42 " pdb=" OG1 THR H 85 " model vdw 2.322 3.120 ... (remaining 123839 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.570 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:7.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.006 0.103 14949 Z= 0.501 Angle : 0.982 17.478 21219 Z= 0.716 Chirality : 0.057 0.540 2427 Planarity : 0.006 0.077 1841 Dihedral : 25.984 97.690 6227 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 6.25 % 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: 0.60 (0.23), residues: 1133 helix: 1.05 (0.18), residues: 673 sheet: 0.23 (0.47), residues: 112 loop : -0.69 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 42 TYR 0.030 0.003 TYR L 248 PHE 0.019 0.003 PHE K 152 TRP 0.030 0.005 TRP L 285 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.50 (14949) covalent geometry : angle 0.98168 / 0.72 (21219) hydrogen bonds : bond 0.11690 / 7.52 ( 874) hydrogen bonds : angle 4.80135 / 3.50 ( 2273) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 MET cc_start: 0.9162 (tpp) cc_final: 0.8955 (tpp) REVERT: G 36 LYS cc_start: 0.8749 (mmpt) cc_final: 0.8481 (mmmm) REVERT: G 75 LYS cc_start: 0.8724 (mmtm) cc_final: 0.8382 (mmtp) REVERT: H 73 GLU cc_start: 0.8281 (tp30) cc_final: 0.8053 (tp30) REVERT: L 248 TYR cc_start: 0.8316 (p90) cc_final: 0.8056 (p90) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.6381 time to fit residues: 202.3298 Evaluate side-chains 256 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 0.0570 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN D 92 GLN E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN H 64 ASN H 106 HIS L 280 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.102638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.068246 restraints weight = 29594.042| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.00 r_work: 0.2806 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14949 Z= 0.146 Angle : 0.670 10.963 21219 Z= 0.378 Chirality : 0.046 0.219 2427 Planarity : 0.005 0.054 1841 Dihedral : 29.727 101.371 3938 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.13 % Allowed : 14.53 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.34 (0.24), residues: 1133 helix: 1.70 (0.19), residues: 679 sheet: 0.32 (0.44), residues: 113 loop : -0.50 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.015 0.002 TYR F 88 PHE 0.026 0.002 PHE K 182 TRP 0.017 0.002 TRP L 42 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (14949) covalent geometry : angle 0.66977 / 0.38 (21219) hydrogen bonds : bond 0.04586 / 2.97 ( 874) hydrogen bonds : angle 3.85743 / 2.84 ( 2273) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 260 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8587 (t0) cc_final: 0.8383 (t0) REVERT: C 90 ASP cc_start: 0.8486 (t70) cc_final: 0.7739 (t70) REVERT: C 92 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8280 (pm20) REVERT: D 102 GLU cc_start: 0.8366 (tp30) cc_final: 0.7895 (tp30) REVERT: E 59 GLU cc_start: 0.8873 (pm20) cc_final: 0.8557 (pm20) REVERT: E 120 MET cc_start: 0.9455 (OUTLIER) cc_final: 0.8318 (mtp) REVERT: F 91 LYS cc_start: 0.9435 (ttpp) cc_final: 0.9114 (ttmt) REVERT: G 36 LYS cc_start: 0.9146 (mmpt) cc_final: 0.8779 (mmmm) REVERT: K 148 PHE cc_start: 0.8385 (m-80) cc_final: 0.7972 (m-80) REVERT: K 171 ARG cc_start: 0.8203 (mtm180) cc_final: 0.7626 (mpp80) REVERT: K 189 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8538 (tt) REVERT: M 38 MET cc_start: 0.8984 (mmp) cc_final: 0.8282 (pp-130) REVERT: M 78 PHE cc_start: 0.9089 (m-80) cc_final: 0.8884 (m-80) outliers start: 21 outliers final: 6 residues processed: 268 average time/residue: 0.6355 time to fit residues: 183.9674 Evaluate side-chains 246 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 238 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain M residue 87 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 37 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN C 31 HIS H 60 ASN H 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.097873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.062297 restraints weight = 29505.528| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.97 r_work: 0.2646 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 14949 Z= 0.276 Angle : 0.732 11.028 21219 Z= 0.396 Chirality : 0.050 0.227 2427 Planarity : 0.005 0.078 1841 Dihedral : 29.782 105.251 3938 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.15 % Allowed : 16.36 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.49 (0.24), residues: 1133 helix: 1.83 (0.19), residues: 679 sheet: 0.40 (0.48), residues: 112 loop : -0.46 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 107 TYR 0.016 0.002 TYR L 229 PHE 0.030 0.002 PHE K 182 TRP 0.007 0.001 TRP L 42 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.28 (14949) covalent geometry : angle 0.73195 / 0.40 (21219) hydrogen bonds : bond 0.05315 / 3.50 ( 874) hydrogen bonds : angle 3.67163 / 2.72 ( 2273) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8596 (mm-30) REVERT: A 120 MET cc_start: 0.9417 (OUTLIER) cc_final: 0.8540 (mtp) REVERT: A 133 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: B 91 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8899 (ttmt) REVERT: E 42 ARG cc_start: 0.8763 (mtp-110) cc_final: 0.8536 (mtp-110) REVERT: E 59 GLU cc_start: 0.8895 (pm20) cc_final: 0.8568 (pm20) REVERT: E 120 MET cc_start: 0.9481 (OUTLIER) cc_final: 0.8648 (mtm) REVERT: G 36 LYS cc_start: 0.9262 (mmpt) cc_final: 0.8901 (mmmm) REVERT: G 104 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8648 (mm110) REVERT: K 95 ASN cc_start: 0.9139 (t0) cc_final: 0.8897 (t0) REVERT: K 148 PHE cc_start: 0.8422 (m-80) cc_final: 0.8097 (m-80) REVERT: K 182 PHE cc_start: 0.6451 (t80) cc_final: 0.6239 (t80) REVERT: K 189 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8573 (tt) REVERT: K 225 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8379 (pm20) REVERT: L 248 TYR cc_start: 0.8454 (p90) cc_final: 0.8096 (p90) REVERT: M 74 ASP cc_start: 0.8342 (t0) cc_final: 0.8064 (t0) outliers start: 31 outliers final: 6 residues processed: 243 average time/residue: 0.6719 time to fit residues: 175.8177 Evaluate side-chains 232 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 221 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 225 GLN Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 87 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 56 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN K 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.099386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.064101 restraints weight = 29516.116| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.96 r_work: 0.2696 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14949 Z= 0.148 Angle : 0.650 11.126 21219 Z= 0.358 Chirality : 0.045 0.224 2427 Planarity : 0.004 0.045 1841 Dihedral : 29.601 107.482 3938 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.44 % Allowed : 18.29 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.74 (0.24), residues: 1133 helix: 2.06 (0.19), residues: 677 sheet: 0.25 (0.47), residues: 117 loop : -0.33 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.021 0.001 TYR K 94 PHE 0.018 0.001 PHE K 182 TRP 0.009 0.001 TRP L 42 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (14949) covalent geometry : angle 0.65048 / 0.36 (21219) hydrogen bonds : bond 0.03921 / 2.54 ( 874) hydrogen bonds : angle 3.54457 / 2.61 ( 2273) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 243 time to evaluate : 0.334 Fit side-chains REVERT: A 94 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8581 (mm-30) REVERT: A 133 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: E 42 ARG cc_start: 0.8786 (mtp-110) cc_final: 0.8555 (mtp-110) REVERT: E 59 GLU cc_start: 0.8874 (pm20) cc_final: 0.8524 (pm20) REVERT: E 120 MET cc_start: 0.9458 (OUTLIER) cc_final: 0.8772 (mtm) REVERT: G 36 LYS cc_start: 0.9256 (mmpt) cc_final: 0.8901 (mmmm) REVERT: G 104 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8663 (mm110) REVERT: K 95 ASN cc_start: 0.9048 (t0) cc_final: 0.8812 (t0) REVERT: K 148 PHE cc_start: 0.8481 (m-80) cc_final: 0.8038 (m-80) REVERT: K 189 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8529 (tt) REVERT: K 225 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8378 (pm20) REVERT: L 248 TYR cc_start: 0.8510 (p90) cc_final: 0.8130 (p90) REVERT: M 21 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8692 (p0) REVERT: M 38 MET cc_start: 0.8984 (mmp) cc_final: 0.8262 (pp-130) REVERT: M 78 PHE cc_start: 0.9204 (m-80) cc_final: 0.8935 (m-80) REVERT: M 87 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8468 (p) outliers start: 24 outliers final: 4 residues processed: 254 average time/residue: 0.6577 time to fit residues: 180.3557 Evaluate side-chains 243 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 233 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 225 GLN Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 87 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 27 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 68 optimal weight: 0.0000 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.0570 chunk 40 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 overall best weight: 0.8506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN H 46 HIS K 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.100372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.065233 restraints weight = 29712.985| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.99 r_work: 0.2730 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14949 Z= 0.131 Angle : 0.615 11.180 21219 Z= 0.346 Chirality : 0.043 0.225 2427 Planarity : 0.004 0.065 1841 Dihedral : 29.224 109.080 3938 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.13 % Allowed : 19.21 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.99 (0.24), residues: 1133 helix: 2.27 (0.19), residues: 675 sheet: 0.50 (0.48), residues: 112 loop : -0.28 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.019 0.001 TYR K 195 PHE 0.027 0.001 PHE K 182 TRP 0.011 0.001 TRP L 42 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 (14949) covalent geometry : angle 0.61503 / 0.35 (21219) hydrogen bonds : bond 0.03675 / 2.39 ( 874) hydrogen bonds : angle 3.43083 / 2.52 ( 2273) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 243 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8467 (mm-30) REVERT: C 62 ILE cc_start: 0.9514 (mt) cc_final: 0.9275 (tt) REVERT: C 104 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8850 (mm-40) REVERT: D 90 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: E 42 ARG cc_start: 0.8774 (mtp-110) cc_final: 0.8556 (mtp-110) REVERT: E 59 GLU cc_start: 0.8827 (pm20) cc_final: 0.8440 (pm20) REVERT: E 120 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.9201 (mtt) REVERT: H 73 GLU cc_start: 0.9174 (tp30) cc_final: 0.8874 (tp30) REVERT: K 69 ASN cc_start: 0.6720 (t0) cc_final: 0.6486 (t0) REVERT: K 148 PHE cc_start: 0.8463 (m-80) cc_final: 0.7996 (m-80) REVERT: K 182 PHE cc_start: 0.6326 (t80) cc_final: 0.6088 (t80) REVERT: K 225 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8390 (pm20) REVERT: M 21 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8679 (p0) REVERT: M 78 PHE cc_start: 0.9214 (m-80) cc_final: 0.8938 (m-80) outliers start: 21 outliers final: 4 residues processed: 255 average time/residue: 0.6365 time to fit residues: 175.6456 Evaluate side-chains 242 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 234 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 225 GLN Chi-restraints excluded: chain M residue 21 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.099809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.064567 restraints weight = 29497.384| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.98 r_work: 0.2715 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14949 Z= 0.146 Angle : 0.621 11.493 21219 Z= 0.347 Chirality : 0.043 0.230 2427 Planarity : 0.004 0.053 1841 Dihedral : 29.177 109.903 3938 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.85 % Allowed : 19.72 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.08 (0.24), residues: 1133 helix: 2.30 (0.19), residues: 678 sheet: 0.63 (0.49), residues: 112 loop : -0.21 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.010 0.001 TYR F 51 PHE 0.020 0.001 PHE K 182 TRP 0.007 0.001 TRP L 42 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (14949) covalent geometry : angle 0.62114 / 0.35 (21219) hydrogen bonds : bond 0.03703 / 2.41 ( 874) hydrogen bonds : angle 3.38740 / 2.49 ( 2273) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: C 62 ILE cc_start: 0.9530 (mt) cc_final: 0.9282 (tt) REVERT: C 64 GLU cc_start: 0.8920 (tt0) cc_final: 0.8591 (tp30) REVERT: E 42 ARG cc_start: 0.8805 (mtp-110) cc_final: 0.8589 (mtp-110) REVERT: E 59 GLU cc_start: 0.8840 (pm20) cc_final: 0.8454 (pm20) REVERT: E 120 MET cc_start: 0.9407 (OUTLIER) cc_final: 0.9081 (mtt) REVERT: F 77 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9076 (mtmp) REVERT: G 36 LYS cc_start: 0.9233 (mmpt) cc_final: 0.8896 (mmmm) REVERT: H 73 GLU cc_start: 0.9199 (tp30) cc_final: 0.8899 (tp30) REVERT: K 148 PHE cc_start: 0.8436 (m-80) cc_final: 0.7971 (m-80) REVERT: K 225 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8402 (pm20) REVERT: L 12 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8697 (mt) REVERT: M 21 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8698 (p0) REVERT: M 78 PHE cc_start: 0.9233 (m-80) cc_final: 0.8950 (m-80) outliers start: 28 outliers final: 9 residues processed: 253 average time/residue: 0.6599 time to fit residues: 180.8826 Evaluate side-chains 246 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 232 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 156 LYS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 225 GLN Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 62 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 51 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN C 73 ASN K 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.097052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.061663 restraints weight = 29199.577| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.93 r_work: 0.2625 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14949 Z= 0.263 Angle : 0.708 11.738 21219 Z= 0.381 Chirality : 0.048 0.232 2427 Planarity : 0.005 0.076 1841 Dihedral : 29.419 114.341 3938 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.05 % Allowed : 20.12 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.82 (0.24), residues: 1133 helix: 2.10 (0.19), residues: 679 sheet: 0.11 (0.47), residues: 122 loop : -0.19 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 83 TYR 0.028 0.002 TYR K 195 PHE 0.022 0.002 PHE G 25 TRP 0.011 0.002 TRP L 42 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.26 (14949) covalent geometry : angle 0.70794 / 0.38 (21219) hydrogen bonds : bond 0.04806 / 3.16 ( 874) hydrogen bonds : angle 3.48359 / 2.57 ( 2273) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: C 62 ILE cc_start: 0.9565 (mt) cc_final: 0.9306 (tt) REVERT: C 64 GLU cc_start: 0.9001 (tt0) cc_final: 0.8675 (tp30) REVERT: D 90 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8442 (mp0) REVERT: E 59 GLU cc_start: 0.8885 (pm20) cc_final: 0.8523 (pm20) REVERT: G 36 LYS cc_start: 0.9239 (mmpt) cc_final: 0.8887 (mmmm) REVERT: H 73 GLU cc_start: 0.9220 (tp30) cc_final: 0.8919 (tp30) REVERT: K 148 PHE cc_start: 0.8432 (m-80) cc_final: 0.8013 (m-80) REVERT: K 151 LYS cc_start: 0.7528 (mmmt) cc_final: 0.7272 (mmmm) REVERT: L 12 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8739 (mp) REVERT: M 78 PHE cc_start: 0.9210 (m-80) cc_final: 0.8888 (m-80) outliers start: 30 outliers final: 16 residues processed: 247 average time/residue: 0.6654 time to fit residues: 177.4430 Evaluate side-chains 245 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 156 LYS Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 225 GLN Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 83 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 4 optimal weight: 0.2980 chunk 126 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN C 73 ASN K 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.098596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.063375 restraints weight = 29383.445| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.95 r_work: 0.2673 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14949 Z= 0.137 Angle : 0.677 13.398 21219 Z= 0.367 Chirality : 0.046 0.247 2427 Planarity : 0.005 0.091 1841 Dihedral : 29.367 115.014 3938 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.34 % Allowed : 21.24 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.84 (0.24), residues: 1133 helix: 2.10 (0.19), residues: 679 sheet: 0.29 (0.48), residues: 119 loop : -0.22 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 42 TYR 0.017 0.002 TYR G 57 PHE 0.043 0.002 PHE K 152 TRP 0.008 0.001 TRP L 42 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (14949) covalent geometry : angle 0.67660 / 0.37 (21219) hydrogen bonds : bond 0.03935 / 2.57 ( 874) hydrogen bonds : angle 3.46657 / 2.56 ( 2273) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 237 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.9077 (tttp) cc_final: 0.8823 (tttp) REVERT: A 133 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: C 62 ILE cc_start: 0.9553 (mt) cc_final: 0.9309 (tt) REVERT: C 64 GLU cc_start: 0.8957 (tt0) cc_final: 0.8631 (tp30) REVERT: C 104 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8849 (mm110) REVERT: D 90 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8431 (mp0) REVERT: E 59 GLU cc_start: 0.8873 (pm20) cc_final: 0.8505 (pm20) REVERT: G 36 LYS cc_start: 0.9228 (mmpt) cc_final: 0.8874 (mmmm) REVERT: H 73 GLU cc_start: 0.9188 (tp30) cc_final: 0.8913 (tp30) REVERT: K 148 PHE cc_start: 0.8409 (m-80) cc_final: 0.7939 (m-80) REVERT: K 195 TYR cc_start: 0.9053 (t80) cc_final: 0.8610 (t80) REVERT: L 12 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8755 (mt) REVERT: M 78 PHE cc_start: 0.9228 (m-80) cc_final: 0.8956 (m-80) outliers start: 23 outliers final: 13 residues processed: 248 average time/residue: 0.6533 time to fit residues: 175.0393 Evaluate side-chains 249 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 156 LYS Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 225 GLN Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 244 MET Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 83 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 13 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN H 60 ASN K 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.098683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.063355 restraints weight = 29249.636| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.95 r_work: 0.2679 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14949 Z= 0.153 Angle : 0.659 12.830 21219 Z= 0.361 Chirality : 0.044 0.225 2427 Planarity : 0.004 0.051 1841 Dihedral : 29.176 115.312 3938 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.34 % Allowed : 22.05 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.90 (0.25), residues: 1133 helix: 2.17 (0.19), residues: 679 sheet: 0.26 (0.49), residues: 119 loop : -0.20 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 42 TYR 0.029 0.002 TYR F 88 PHE 0.026 0.002 PHE K 152 TRP 0.011 0.001 TRP L 42 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (14949) covalent geometry : angle 0.65920 / 0.36 (21219) hydrogen bonds : bond 0.03742 / 2.43 ( 874) hydrogen bonds : angle 3.43657 / 2.53 ( 2273) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 239 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.9067 (tttp) cc_final: 0.8810 (tttp) REVERT: A 133 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: C 62 ILE cc_start: 0.9550 (mt) cc_final: 0.9311 (tt) REVERT: C 64 GLU cc_start: 0.8962 (tt0) cc_final: 0.8642 (tp30) REVERT: C 104 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8850 (mm110) REVERT: D 90 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8447 (mp0) REVERT: E 59 GLU cc_start: 0.8870 (pm20) cc_final: 0.8495 (pm20) REVERT: G 36 LYS cc_start: 0.9232 (mmpt) cc_final: 0.8882 (mmmm) REVERT: H 73 GLU cc_start: 0.9184 (tp30) cc_final: 0.8870 (tp30) REVERT: K 148 PHE cc_start: 0.8413 (m-80) cc_final: 0.7960 (m-80) REVERT: K 195 TYR cc_start: 0.9035 (t80) cc_final: 0.8629 (t80) REVERT: L 12 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8736 (mp) REVERT: M 78 PHE cc_start: 0.9208 (m-80) cc_final: 0.8933 (m-80) outliers start: 23 outliers final: 11 residues processed: 250 average time/residue: 0.6433 time to fit residues: 174.0769 Evaluate side-chains 251 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 237 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 156 LYS Chi-restraints excluded: chain K residue 225 GLN Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 244 MET Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 83 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 80 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN B 25 ASN C 73 ASN K 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.097822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.062561 restraints weight = 29410.090| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.93 r_work: 0.2657 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14949 Z= 0.206 Angle : 0.687 12.931 21219 Z= 0.371 Chirality : 0.045 0.233 2427 Planarity : 0.005 0.049 1841 Dihedral : 29.178 116.846 3938 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.13 % Allowed : 22.97 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.86 (0.24), residues: 1133 helix: 2.15 (0.19), residues: 678 sheet: 0.21 (0.49), residues: 119 loop : -0.24 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 220 TYR 0.019 0.002 TYR G 57 PHE 0.026 0.002 PHE K 182 TRP 0.014 0.002 TRP L 42 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.21 (14949) covalent geometry : angle 0.68720 / 0.37 (21219) hydrogen bonds : bond 0.04073 / 2.65 ( 874) hydrogen bonds : angle 3.45189 / 2.54 ( 2273) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.9065 (tttp) cc_final: 0.8812 (tttp) REVERT: A 133 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: C 62 ILE cc_start: 0.9560 (mt) cc_final: 0.9315 (tt) REVERT: C 64 GLU cc_start: 0.9008 (tt0) cc_final: 0.8686 (tp30) REVERT: D 90 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: E 59 GLU cc_start: 0.8872 (pm20) cc_final: 0.8485 (pm20) REVERT: G 36 LYS cc_start: 0.9235 (mmpt) cc_final: 0.8910 (mmmm) REVERT: H 73 GLU cc_start: 0.9199 (tp30) cc_final: 0.8885 (tp30) REVERT: K 148 PHE cc_start: 0.8440 (m-80) cc_final: 0.7990 (m-80) REVERT: K 195 TYR cc_start: 0.9049 (t80) cc_final: 0.8649 (t80) REVERT: L 12 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8784 (mp) REVERT: M 78 PHE cc_start: 0.9212 (m-80) cc_final: 0.8950 (m-80) outliers start: 21 outliers final: 14 residues processed: 243 average time/residue: 0.6557 time to fit residues: 172.2435 Evaluate side-chains 250 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 156 LYS Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 225 GLN Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 244 MET Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 83 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 105 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN B 25 ASN C 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.097545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.062266 restraints weight = 29455.627| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.94 r_work: 0.2645 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14949 Z= 0.213 Angle : 0.697 12.820 21219 Z= 0.376 Chirality : 0.045 0.236 2427 Planarity : 0.005 0.045 1841 Dihedral : 29.217 120.292 3938 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.93 % Allowed : 23.27 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.77 (0.24), residues: 1133 helix: 2.07 (0.19), residues: 680 sheet: 0.18 (0.49), residues: 117 loop : -0.26 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 42 TYR 0.033 0.002 TYR F 88 PHE 0.027 0.002 PHE K 182 TRP 0.015 0.002 TRP L 42 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (14949) covalent geometry : angle 0.69701 / 0.38 (21219) hydrogen bonds : bond 0.04013 / 2.62 ( 874) hydrogen bonds : angle 3.46050 / 2.55 ( 2273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5755.42 seconds wall clock time: 98 minutes 26.45 seconds (5906.45 seconds total)