Starting phenix.real_space_refine on Wed Mar 4 12:51:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oha_12898/03_2026/7oha_12898.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oha_12898/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7oha_12898/03_2026/7oha_12898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oha_12898/03_2026/7oha_12898.map" model { file = "/net/cci-nas-00/data/ceres_data/7oha_12898/03_2026/7oha_12898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oha_12898/03_2026/7oha_12898.cif" } 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-dev-5986/lib/python3.9/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: 2.91, per 1000 atoms: 0.20 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: 1.06 Conformation dependent library (CDL) restraints added in 437.1 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: 2.07 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: 2.61 Time building geometry restraints manager: 1.47 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=" CG LEU L 46 " pdb=" CD1 LEU L 46 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.90e+00 bond pdb=" CG1 ILE M 113 " pdb=" CD1 ILE M 113 " ideal model delta sigma weight residual 1.513 1.410 0.103 3.90e-02 6.57e+02 6.94e+00 bond pdb=" CB VAL L 267 " pdb=" CG1 VAL L 267 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.42e+00 bond pdb=" CG1 ILE L 13 " pdb=" CD1 ILE L 13 " ideal model delta sigma weight residual 1.513 1.435 0.078 3.90e-02 6.57e+02 3.96e+00 bond pdb=" CD GLN K 225 " pdb=" OE1 GLN K 225 " ideal model delta sigma weight residual 1.231 1.196 0.035 1.90e-02 2.77e+03 3.41e+00 ... (remaining 14944 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 21037 3.50 - 6.99: 160 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=" 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 angle pdb=" CG1 ILE L 12 " pdb=" CB ILE L 12 " pdb=" CG2 ILE L 12 " ideal model delta sigma weight residual 110.70 96.08 14.62 3.00e+00 1.11e-01 2.37e+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: 2283 0.108 - 0.216: 130 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 14.100 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.005 0.103 14949 Z= 0.231 Angle : 0.910 17.478 21219 Z= 0.524 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 covalent geometry : bond 0.00493 (14949) covalent geometry : angle 0.90979 (21219) hydrogen bonds : bond 0.11690 ( 874) hydrogen bonds : angle 4.80135 ( 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 : 0.451 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: 0.8057 (p90) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.7176 time to fit residues: 226.4981 Evaluate side-chains 257 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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: 5.9990 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: 4.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 92 GLN E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN H 64 ASN ** L 280 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 = 0.3639 r_free = 0.3639 target = 0.102339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.067844 restraints weight = 29556.328| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.98 r_work: 0.2786 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14949 Z= 0.165 Angle : 0.584 11.356 21219 Z= 0.341 Chirality : 0.037 0.192 2427 Planarity : 0.004 0.059 1841 Dihedral : 28.998 95.257 3938 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.24 % Allowed : 13.92 % Favored : 83.84 % 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: 1.61 (0.24), residues: 1133 helix: 1.91 (0.19), residues: 678 sheet: 0.49 (0.46), residues: 117 loop : -0.40 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.011 0.001 TYR F 51 PHE 0.024 0.002 PHE K 182 TRP 0.014 0.002 TRP L 42 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00361 (14949) covalent geometry : angle 0.58398 (21219) hydrogen bonds : bond 0.03588 ( 874) hydrogen bonds : angle 3.46356 ( 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 288 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 266 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9539 (p) cc_final: 0.9197 (t) REVERT: A 94 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8459 (mm-30) REVERT: A 133 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: B 79 LYS cc_start: 0.9300 (mtmm) cc_final: 0.9093 (mttt) REVERT: C 90 ASP cc_start: 0.8601 (t70) cc_final: 0.7830 (t70) REVERT: C 92 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8274 (pm20) REVERT: D 56 MET cc_start: 0.9568 (tpp) cc_final: 0.9356 (tpp) REVERT: D 102 GLU cc_start: 0.8525 (tp30) cc_final: 0.8137 (tp30) REVERT: E 59 GLU cc_start: 0.8919 (pm20) cc_final: 0.8608 (pm20) REVERT: E 120 MET cc_start: 0.9523 (OUTLIER) cc_final: 0.8519 (mtm) REVERT: F 49 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8994 (mm) REVERT: F 91 LYS cc_start: 0.9419 (ttpp) cc_final: 0.9160 (ttmt) REVERT: G 36 LYS cc_start: 0.9226 (mmpt) cc_final: 0.8837 (mmmm) REVERT: G 104 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8645 (mm110) REVERT: H 73 GLU cc_start: 0.9213 (tp30) cc_final: 0.8991 (tp30) REVERT: K 95 ASN cc_start: 0.9008 (t0) cc_final: 0.8727 (t0) REVERT: K 148 PHE cc_start: 0.8319 (m-80) cc_final: 0.8012 (m-80) REVERT: K 171 ARG cc_start: 0.8285 (mtm180) cc_final: 0.8006 (mpp80) REVERT: K 189 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8475 (tt) REVERT: L 244 MET cc_start: 0.8087 (ttm) cc_final: 0.7821 (ttm) REVERT: L 258 TRP cc_start: 0.8082 (m100) cc_final: 0.7880 (t-100) outliers start: 22 outliers final: 5 residues processed: 273 average time/residue: 0.7361 time to fit residues: 216.6922 Evaluate side-chains 254 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 245 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 84 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 M residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 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 68 GLN A 125 GLN C 31 HIS K 69 ASN K 91 ASN ** L 280 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 = 0.3560 r_free = 0.3560 target = 0.098264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.062735 restraints weight = 29558.816| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.99 r_work: 0.2656 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14949 Z= 0.255 Angle : 0.610 10.511 21219 Z= 0.351 Chirality : 0.040 0.172 2427 Planarity : 0.005 0.070 1841 Dihedral : 29.160 96.369 3938 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.05 % Allowed : 16.57 % Favored : 80.39 % 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: 1.75 (0.24), residues: 1133 helix: 2.03 (0.19), residues: 678 sheet: 0.47 (0.47), residues: 117 loop : -0.33 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 83 TYR 0.013 0.002 TYR K 195 PHE 0.024 0.002 PHE K 182 TRP 0.018 0.002 TRP L 42 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00582 (14949) covalent geometry : angle 0.61023 (21219) hydrogen bonds : bond 0.03959 ( 874) hydrogen bonds : angle 3.42797 ( 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 274 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9555 (p) cc_final: 0.9343 (t) REVERT: A 94 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8492 (mm-30) REVERT: A 120 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8591 (mtp) REVERT: A 133 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: D 90 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8468 (mp0) REVERT: E 59 GLU cc_start: 0.8945 (pm20) cc_final: 0.8608 (pm20) REVERT: E 120 MET cc_start: 0.9398 (OUTLIER) cc_final: 0.8962 (mtt) REVERT: F 88 TYR cc_start: 0.9325 (m-10) cc_final: 0.9122 (m-10) REVERT: G 36 LYS cc_start: 0.9297 (mmpt) cc_final: 0.8939 (mmmm) REVERT: G 104 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8638 (mm110) REVERT: H 73 GLU cc_start: 0.9245 (tp30) cc_final: 0.9025 (tp30) REVERT: K 69 ASN cc_start: 0.6658 (t0) cc_final: 0.6418 (t0) REVERT: K 95 ASN cc_start: 0.9106 (t0) cc_final: 0.8863 (t0) REVERT: K 141 ARG cc_start: 0.8646 (mmm-85) cc_final: 0.8311 (ttp80) REVERT: K 148 PHE cc_start: 0.8346 (m-80) cc_final: 0.7989 (m-80) REVERT: K 171 ARG cc_start: 0.8360 (mtm180) cc_final: 0.7979 (mpp80) REVERT: K 189 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8535 (tt) REVERT: K 225 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: K 238 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7785 (ttm-80) REVERT: L 248 TYR cc_start: 0.8519 (p90) cc_final: 0.8105 (p90) REVERT: M 21 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8725 (p0) REVERT: M 74 ASP cc_start: 0.8320 (t0) cc_final: 0.7964 (t0) REVERT: M 78 PHE cc_start: 0.9216 (m-80) cc_final: 0.8916 (m-80) outliers start: 30 outliers final: 11 residues processed: 258 average time/residue: 0.8204 time to fit residues: 226.5107 Evaluate side-chains 245 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 56 GLU 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 F residue 79 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 189 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 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: 1.9990 chunk 69 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN H 46 HIS L 280 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.100415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.065230 restraints weight = 29652.121| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.98 r_work: 0.2733 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14949 Z= 0.150 Angle : 0.560 11.086 21219 Z= 0.326 Chirality : 0.036 0.163 2427 Planarity : 0.004 0.048 1841 Dihedral : 28.674 96.897 3938 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.25 % Allowed : 18.29 % Favored : 78.46 % 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: 2.11 (0.24), residues: 1133 helix: 2.33 (0.19), residues: 675 sheet: 0.58 (0.49), residues: 116 loop : -0.19 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.015 0.001 TYR G 57 PHE 0.024 0.001 PHE K 182 TRP 0.017 0.002 TRP L 42 HIS 0.003 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00329 (14949) covalent geometry : angle 0.55957 (21219) hydrogen bonds : bond 0.03238 ( 874) hydrogen bonds : angle 3.27826 ( 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 281 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.9073 (tttp) cc_final: 0.8828 (tttp) REVERT: A 94 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8391 (mm-30) REVERT: C 62 ILE cc_start: 0.9519 (mt) cc_final: 0.9270 (tt) REVERT: D 90 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8475 (mp0) REVERT: E 59 GLU cc_start: 0.8929 (pm20) cc_final: 0.8586 (pm20) REVERT: E 120 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.9075 (mtt) REVERT: F 77 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9114 (mtmp) REVERT: G 36 LYS cc_start: 0.9265 (mmpt) cc_final: 0.8923 (mmmm) REVERT: G 104 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8580 (mm110) REVERT: H 73 GLU cc_start: 0.9209 (tp30) cc_final: 0.8953 (tp30) REVERT: K 90 ARG cc_start: 0.8403 (ptt180) cc_final: 0.8072 (ptt180) REVERT: K 95 ASN cc_start: 0.9081 (t0) cc_final: 0.8838 (t0) REVERT: K 148 PHE cc_start: 0.8401 (m-80) cc_final: 0.7982 (m-80) REVERT: L 12 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8722 (mt) REVERT: L 248 TYR cc_start: 0.8484 (p90) cc_final: 0.8133 (p90) REVERT: M 21 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8726 (p0) REVERT: M 74 ASP cc_start: 0.8394 (t0) cc_final: 0.7999 (t0) REVERT: M 78 PHE cc_start: 0.9222 (m-80) cc_final: 0.8932 (m-80) outliers start: 32 outliers final: 6 residues processed: 266 average time/residue: 0.7217 time to fit residues: 206.9084 Evaluate side-chains 251 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 240 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 225 GLN Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain M residue 21 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 27 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 C 104 GLN K 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.099400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.064251 restraints weight = 29469.623| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.94 r_work: 0.2688 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14949 Z= 0.188 Angle : 0.573 11.373 21219 Z= 0.330 Chirality : 0.037 0.174 2427 Planarity : 0.004 0.048 1841 Dihedral : 28.714 96.724 3938 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.46 % Allowed : 18.90 % Favored : 77.64 % 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: 2.10 (0.24), residues: 1133 helix: 2.32 (0.19), residues: 679 sheet: 0.23 (0.48), residues: 124 loop : -0.08 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 83 TYR 0.022 0.001 TYR K 195 PHE 0.025 0.001 PHE K 182 TRP 0.021 0.002 TRP L 42 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00425 (14949) covalent geometry : angle 0.57293 (21219) hydrogen bonds : bond 0.03403 ( 874) hydrogen bonds : angle 3.27652 ( 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 272 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.9082 (tttp) cc_final: 0.8812 (tttp) REVERT: A 94 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8482 (mm-30) REVERT: A 133 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: C 62 ILE cc_start: 0.9550 (mt) cc_final: 0.9307 (tt) REVERT: D 90 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8448 (mp0) REVERT: E 59 GLU cc_start: 0.8940 (pm20) cc_final: 0.8562 (pm20) REVERT: G 36 LYS cc_start: 0.9258 (mmpt) cc_final: 0.8907 (mmmm) REVERT: G 104 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8614 (mm110) REVERT: H 73 GLU cc_start: 0.9212 (tp30) cc_final: 0.8965 (tp30) REVERT: K 90 ARG cc_start: 0.8392 (ptt180) cc_final: 0.8106 (ptt180) REVERT: K 95 ASN cc_start: 0.9060 (t0) cc_final: 0.8840 (t0) REVERT: K 148 PHE cc_start: 0.8504 (m-80) cc_final: 0.8030 (m-80) REVERT: K 151 LYS cc_start: 0.7592 (mmmt) cc_final: 0.7384 (mmmm) REVERT: K 156 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8708 (ptmm) REVERT: L 12 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8816 (mt) REVERT: L 278 LYS cc_start: 0.8235 (pptt) cc_final: 0.8016 (pmtt) REVERT: M 78 PHE cc_start: 0.9215 (m-80) cc_final: 0.8903 (m-80) outliers start: 34 outliers final: 14 residues processed: 258 average time/residue: 0.7099 time to fit residues: 197.2077 Evaluate side-chains 253 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 235 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 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 F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 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 68 THR Chi-restraints excluded: chain M residue 83 CYS 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: 8.9990 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN 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 = 0.3593 r_free = 0.3593 target = 0.100070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.065055 restraints weight = 29289.062| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.94 r_work: 0.2706 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14949 Z= 0.155 Angle : 0.572 12.045 21219 Z= 0.330 Chirality : 0.036 0.174 2427 Planarity : 0.004 0.050 1841 Dihedral : 28.663 96.968 3938 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.05 % Allowed : 20.02 % Favored : 76.93 % 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: 2.10 (0.24), residues: 1133 helix: 2.34 (0.19), residues: 678 sheet: 0.16 (0.47), residues: 124 loop : -0.07 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.024 0.001 TYR K 195 PHE 0.020 0.001 PHE K 155 TRP 0.020 0.001 TRP L 42 HIS 0.006 0.001 HIS K 88 Details of bonding type rmsd covalent geometry : bond 0.00345 (14949) covalent geometry : angle 0.57244 (21219) hydrogen bonds : bond 0.03246 ( 874) hydrogen bonds : angle 3.30048 ( 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 268 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.9064 (tttp) cc_final: 0.8790 (tttp) REVERT: C 62 ILE cc_start: 0.9530 (mt) cc_final: 0.9290 (tt) REVERT: C 104 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8849 (mm110) REVERT: D 90 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: E 59 GLU cc_start: 0.8927 (pm20) cc_final: 0.8553 (pm20) REVERT: H 73 GLU cc_start: 0.9170 (tp30) cc_final: 0.8902 (tp30) REVERT: K 95 ASN cc_start: 0.9045 (t0) cc_final: 0.8818 (t0) REVERT: K 148 PHE cc_start: 0.8493 (m-80) cc_final: 0.8047 (m-80) REVERT: L 12 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8800 (mt) REVERT: M 38 MET cc_start: 0.8966 (mmp) cc_final: 0.8315 (pp-130) REVERT: M 78 PHE cc_start: 0.9201 (m-80) cc_final: 0.8921 (m-80) outliers start: 30 outliers final: 14 residues processed: 254 average time/residue: 0.7351 time to fit residues: 201.0175 Evaluate side-chains 250 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 234 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 120 SER 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 83 CYS Chi-restraints excluded: chain M residue 108 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 51 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 K 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.095205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.059852 restraints weight = 29448.036| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 1.98 r_work: 0.2582 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 14949 Z= 0.365 Angle : 0.675 12.097 21219 Z= 0.381 Chirality : 0.044 0.163 2427 Planarity : 0.005 0.044 1841 Dihedral : 29.283 100.934 3938 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.66 % Allowed : 19.92 % 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: 1.75 (0.24), residues: 1133 helix: 2.02 (0.19), residues: 680 sheet: 0.02 (0.48), residues: 124 loop : -0.12 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 83 TYR 0.013 0.002 TYR L 10 PHE 0.017 0.002 PHE G 25 TRP 0.031 0.003 TRP L 42 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00834 (14949) covalent geometry : angle 0.67493 (21219) hydrogen bonds : bond 0.04461 ( 874) hydrogen bonds : angle 3.48527 ( 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 264 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.9141 (tttp) cc_final: 0.8877 (tttp) REVERT: A 94 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8551 (mm-30) REVERT: A 133 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: D 96 ARG cc_start: 0.9166 (mtt-85) cc_final: 0.8920 (mtt90) REVERT: E 59 GLU cc_start: 0.9013 (pm20) cc_final: 0.8661 (pm20) REVERT: E 120 MET cc_start: 0.9303 (mtt) cc_final: 0.8961 (mtm) REVERT: G 36 LYS cc_start: 0.9270 (mmpt) cc_final: 0.8923 (mmmm) REVERT: G 104 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8738 (mm110) REVERT: H 73 GLU cc_start: 0.9234 (tp30) cc_final: 0.8974 (tp30) REVERT: K 95 ASN cc_start: 0.8937 (t0) cc_final: 0.8710 (t0) REVERT: K 148 PHE cc_start: 0.8537 (m-80) cc_final: 0.8020 (m-80) REVERT: K 190 PHE cc_start: 0.8985 (t80) cc_final: 0.8756 (t80) REVERT: L 12 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8882 (mp) REVERT: L 248 TYR cc_start: 0.8608 (p90) cc_final: 0.8192 (p90) REVERT: M 78 PHE cc_start: 0.9278 (m-80) cc_final: 0.8988 (m-80) outliers start: 36 outliers final: 17 residues processed: 246 average time/residue: 0.7408 time to fit residues: 195.9588 Evaluate side-chains 243 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 224 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS 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 F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 SER 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 Chi-restraints excluded: chain M residue 108 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 0.0470 chunk 132 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.097721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.062484 restraints weight = 29444.521| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.95 r_work: 0.2653 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14949 Z= 0.153 Angle : 0.627 13.239 21219 Z= 0.355 Chirality : 0.039 0.209 2427 Planarity : 0.005 0.091 1841 Dihedral : 29.189 103.157 3938 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.34 % Allowed : 21.75 % Favored : 75.91 % 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: 1.98 (0.19), residues: 681 sheet: 0.14 (0.48), residues: 119 loop : -0.12 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 23 TYR 0.018 0.001 TYR K 195 PHE 0.016 0.002 PHE K 155 TRP 0.030 0.002 TRP L 42 HIS 0.006 0.001 HIS K 88 Details of bonding type rmsd covalent geometry : bond 0.00337 (14949) covalent geometry : angle 0.62671 (21219) hydrogen bonds : bond 0.03676 ( 874) hydrogen bonds : angle 3.43209 ( 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 261 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.9055 (tttp) cc_final: 0.8808 (tttp) REVERT: A 94 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8468 (mm-30) REVERT: C 104 GLN cc_start: 0.9103 (mm-40) cc_final: 0.8855 (mm110) REVERT: E 59 GLU cc_start: 0.9012 (pm20) cc_final: 0.8672 (pm20) REVERT: G 36 LYS cc_start: 0.9235 (mmpt) cc_final: 0.8879 (mmmm) REVERT: H 73 GLU cc_start: 0.9157 (tp30) cc_final: 0.8902 (tp30) REVERT: K 95 ASN cc_start: 0.8893 (t0) cc_final: 0.8658 (t0) REVERT: K 148 PHE cc_start: 0.8472 (m-80) cc_final: 0.7959 (m-80) REVERT: K 190 PHE cc_start: 0.8915 (t80) cc_final: 0.8677 (t80) REVERT: L 12 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8901 (mp) REVERT: L 248 TYR cc_start: 0.8590 (p90) cc_final: 0.8270 (p90) REVERT: M 38 MET cc_start: 0.8920 (mmp) cc_final: 0.8306 (pp-130) REVERT: M 78 PHE cc_start: 0.9234 (m-80) cc_final: 0.8922 (m-80) outliers start: 23 outliers final: 12 residues processed: 249 average time/residue: 0.7029 time to fit residues: 188.5315 Evaluate side-chains 246 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 233 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 88 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 83 CYS Chi-restraints excluded: chain M residue 108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 B 25 ASN C 73 ASN E 113 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.097593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.062552 restraints weight = 29356.744| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.92 r_work: 0.2659 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14949 Z= 0.206 Angle : 0.616 13.307 21219 Z= 0.347 Chirality : 0.038 0.159 2427 Planarity : 0.004 0.049 1841 Dihedral : 28.716 103.054 3938 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.13 % Allowed : 22.56 % Favored : 75.30 % 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: 1.85 (0.24), residues: 1133 helix: 2.12 (0.19), residues: 681 sheet: 0.10 (0.48), residues: 119 loop : -0.15 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 83 TYR 0.035 0.001 TYR F 88 PHE 0.014 0.001 PHE K 155 TRP 0.030 0.002 TRP L 42 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00469 (14949) covalent geometry : angle 0.61618 (21219) hydrogen bonds : bond 0.03540 ( 874) hydrogen bonds : angle 3.36045 ( 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 253 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 ARG cc_start: 0.8451 (ptp-110) cc_final: 0.8152 (mtm110) REVERT: D 96 ARG cc_start: 0.9099 (mtt-85) cc_final: 0.8850 (mtt90) REVERT: E 59 GLU cc_start: 0.9034 (pm20) cc_final: 0.8683 (pm20) REVERT: G 36 LYS cc_start: 0.9240 (mmpt) cc_final: 0.8884 (mmmm) REVERT: H 73 GLU cc_start: 0.9176 (tp30) cc_final: 0.8926 (tp30) REVERT: K 95 ASN cc_start: 0.8891 (t0) cc_final: 0.8675 (t0) REVERT: K 148 PHE cc_start: 0.8540 (m-80) cc_final: 0.7974 (m-80) REVERT: K 190 PHE cc_start: 0.8938 (t80) cc_final: 0.8665 (t80) REVERT: L 248 TYR cc_start: 0.8576 (p90) cc_final: 0.8244 (p90) REVERT: M 74 ASP cc_start: 0.8335 (t0) cc_final: 0.8035 (t0) REVERT: M 78 PHE cc_start: 0.9230 (m-80) cc_final: 0.8914 (m-80) outliers start: 21 outliers final: 14 residues processed: 243 average time/residue: 0.7268 time to fit residues: 189.8207 Evaluate side-chains 247 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 233 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 225 GLN 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 83 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 80 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN E 113 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 = 0.3556 r_free = 0.3556 target = 0.097862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.062821 restraints weight = 29405.235| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.93 r_work: 0.2667 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14949 Z= 0.191 Angle : 0.613 10.905 21219 Z= 0.348 Chirality : 0.038 0.158 2427 Planarity : 0.004 0.059 1841 Dihedral : 28.695 103.091 3938 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.93 % Allowed : 22.87 % Favored : 75.20 % 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 (0.25), residues: 1133 helix: 2.13 (0.19), residues: 680 sheet: 0.13 (0.48), residues: 119 loop : -0.15 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 83 TYR 0.038 0.002 TYR F 88 PHE 0.027 0.002 PHE K 152 TRP 0.033 0.002 TRP L 42 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00433 (14949) covalent geometry : angle 0.61337 (21219) hydrogen bonds : bond 0.03497 ( 874) hydrogen bonds : angle 3.36233 ( 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 252 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 233 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 ARG cc_start: 0.8498 (ptp-110) cc_final: 0.8177 (mtm110) REVERT: D 96 ARG cc_start: 0.9090 (mtt-85) cc_final: 0.8834 (mtt90) REVERT: E 59 GLU cc_start: 0.9003 (pm20) cc_final: 0.8641 (pm20) REVERT: G 36 LYS cc_start: 0.9235 (mmpt) cc_final: 0.8877 (mmmm) REVERT: H 73 GLU cc_start: 0.9186 (tp30) cc_final: 0.8934 (tp30) REVERT: K 95 ASN cc_start: 0.8891 (t0) cc_final: 0.8674 (t0) REVERT: K 148 PHE cc_start: 0.8536 (m-80) cc_final: 0.7999 (m-80) REVERT: K 190 PHE cc_start: 0.8925 (t80) cc_final: 0.8658 (t80) REVERT: K 195 TYR cc_start: 0.9150 (t80) cc_final: 0.8900 (t80) REVERT: M 78 PHE cc_start: 0.9223 (m-80) cc_final: 0.8905 (m-80) outliers start: 19 outliers final: 16 residues processed: 241 average time/residue: 0.7299 time to fit residues: 189.3546 Evaluate side-chains 248 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 232 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 225 GLN 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 83 CYS Chi-restraints excluded: chain M residue 108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 4 optimal weight: 0.4980 chunk 75 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.098070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.062815 restraints weight = 29390.343| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.95 r_work: 0.2677 rms_B_bonded: 3.14 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: 0.8693 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14949 Z= 0.194 Angle : 0.613 13.338 21219 Z= 0.347 Chirality : 0.038 0.142 2427 Planarity : 0.004 0.047 1841 Dihedral : 28.604 103.169 3938 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.44 % Allowed : 22.87 % Favored : 74.70 % 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: 1.92 (0.25), residues: 1133 helix: 2.17 (0.19), residues: 680 sheet: 0.18 (0.49), residues: 119 loop : -0.13 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 83 TYR 0.041 0.002 TYR F 88 PHE 0.025 0.002 PHE K 152 TRP 0.035 0.002 TRP L 42 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00438 (14949) covalent geometry : angle 0.61270 (21219) hydrogen bonds : bond 0.03450 ( 874) hydrogen bonds : angle 3.34632 ( 2273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6357.14 seconds wall clock time: 108 minutes 30.39 seconds (6510.39 seconds total)