Starting phenix.real_space_refine on Thu Jul 31 19:07:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oha_12898/07_2025/7oha_12898.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oha_12898/07_2025/7oha_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_12898/07_2025/7oha_12898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oha_12898/07_2025/7oha_12898.map" model { file = "/net/cci-nas-00/data/ceres_data/7oha_12898/07_2025/7oha_12898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oha_12898/07_2025/7oha_12898.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.91, per 1000 atoms: 0.56 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: 3.08 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 5.72 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: 5.63 Time building geometry restraints manager: 3.74 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 36.070 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.340 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.030 0.005 TRP L 285 HIS 0.007 0.001 HIS F 75 PHE 0.019 0.003 PHE K 152 TYR 0.030 0.003 TYR L 248 ARG 0.011 0.001 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.11690 ( 874) hydrogen bonds : angle 4.80135 ( 2273) covalent geometry : bond 0.00493 (14949) covalent geometry : angle 0.90979 (21219) *********************** 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 : 1.139 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: 1.4100 time to fit residues: 446.9070 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 : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.101307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.066579 restraints weight = 29513.029| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.98 r_work: 0.2756 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14949 Z= 0.181 Angle : 0.591 11.417 21219 Z= 0.344 Chirality : 0.037 0.194 2427 Planarity : 0.004 0.058 1841 Dihedral : 29.087 95.612 3938 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.34 % Allowed : 13.62 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.24), residues: 1133 helix: 1.88 (0.19), residues: 678 sheet: 0.47 (0.46), residues: 117 loop : -0.41 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 42 HIS 0.003 0.001 HIS B 75 PHE 0.024 0.002 PHE K 182 TYR 0.011 0.001 TYR F 51 ARG 0.007 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 874) hydrogen bonds : angle 3.49776 ( 2273) covalent geometry : bond 0.00403 (14949) covalent geometry : angle 0.59123 (21219) *********************** 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: 23 poor density : 258 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9564 (p) cc_final: 0.9208 (t) REVERT: A 94 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8472 (mm-30) REVERT: A 133 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: B 79 LYS cc_start: 0.9309 (mtmm) cc_final: 0.9103 (mttt) REVERT: C 90 ASP cc_start: 0.8609 (t70) cc_final: 0.7827 (t70) REVERT: C 92 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8304 (pm20) REVERT: D 65 ASP cc_start: 0.9171 (t0) cc_final: 0.8959 (t0) REVERT: D 102 GLU cc_start: 0.8595 (tp30) cc_final: 0.8264 (tp30) REVERT: E 42 ARG cc_start: 0.8799 (mtp-110) cc_final: 0.8516 (mtp-110) REVERT: E 59 GLU cc_start: 0.8920 (pm20) cc_final: 0.8618 (pm20) REVERT: E 120 MET cc_start: 0.9515 (OUTLIER) cc_final: 0.8633 (mtm) REVERT: F 49 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9050 (mm) REVERT: G 36 LYS cc_start: 0.9236 (mmpt) cc_final: 0.8888 (mmmm) REVERT: G 104 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8616 (mm110) REVERT: H 73 GLU cc_start: 0.9218 (tp30) cc_final: 0.9002 (tp30) REVERT: K 95 ASN cc_start: 0.9005 (t0) cc_final: 0.8739 (t0) REVERT: K 148 PHE cc_start: 0.8332 (m-80) cc_final: 0.8035 (m-80) REVERT: K 171 ARG cc_start: 0.8296 (mtm180) cc_final: 0.7928 (mpp80) REVERT: K 189 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8495 (tt) REVERT: L 244 MET cc_start: 0.8144 (ttm) cc_final: 0.7876 (ttm) REVERT: L 248 TYR cc_start: 0.8315 (p90) cc_final: 0.7948 (p90) REVERT: L 258 TRP cc_start: 0.8166 (m100) cc_final: 0.7874 (t-100) REVERT: M 74 ASP cc_start: 0.8249 (t0) cc_final: 0.7914 (t0) outliers start: 23 outliers final: 5 residues processed: 266 average time/residue: 1.4844 time to fit residues: 425.7054 Evaluate side-chains 249 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 240 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 67 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 31 HIS H 46 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 = 0.3556 r_free = 0.3556 target = 0.097972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.062706 restraints weight = 29435.014| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.96 r_work: 0.2653 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2421 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= 0.252 Angle : 0.612 10.723 21219 Z= 0.352 Chirality : 0.040 0.170 2427 Planarity : 0.005 0.067 1841 Dihedral : 29.175 97.383 3938 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.46 % Allowed : 16.26 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1133 helix: 2.03 (0.19), residues: 678 sheet: 0.46 (0.46), residues: 119 loop : -0.34 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 42 HIS 0.006 0.001 HIS B 75 PHE 0.023 0.002 PHE K 182 TYR 0.012 0.002 TYR D 37 ARG 0.011 0.001 ARG K 79 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 874) hydrogen bonds : angle 3.44645 ( 2273) covalent geometry : bond 0.00574 (14949) covalent geometry : angle 0.61233 (21219) *********************** 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 277 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9557 (p) cc_final: 0.9337 (t) REVERT: A 94 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8472 (mm-30) REVERT: A 120 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8619 (mtp) REVERT: A 133 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: C 64 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8847 (tt0) REVERT: D 65 ASP cc_start: 0.9242 (t0) cc_final: 0.9008 (t0) REVERT: D 90 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8444 (mp0) REVERT: E 59 GLU cc_start: 0.8925 (pm20) cc_final: 0.8632 (pm20) REVERT: E 120 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.8963 (mtt) REVERT: F 88 TYR cc_start: 0.9308 (m-10) cc_final: 0.9105 (m-10) REVERT: G 36 LYS cc_start: 0.9283 (mmpt) cc_final: 0.8917 (mmmm) REVERT: G 104 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8620 (mm110) REVERT: H 73 GLU cc_start: 0.9228 (tp30) cc_final: 0.9000 (tp30) REVERT: K 95 ASN cc_start: 0.9100 (t0) cc_final: 0.8829 (t0) REVERT: K 141 ARG cc_start: 0.8666 (mmm-85) cc_final: 0.8341 (ttp80) REVERT: K 148 PHE cc_start: 0.8267 (m-80) cc_final: 0.7908 (m-80) REVERT: K 171 ARG cc_start: 0.8364 (mtm180) cc_final: 0.7953 (mpp80) REVERT: K 189 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8545 (tt) REVERT: K 225 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8336 (pm20) REVERT: K 238 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7806 (ttm-80) REVERT: L 248 TYR cc_start: 0.8540 (p90) cc_final: 0.8187 (p90) REVERT: M 21 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8732 (p0) REVERT: M 74 ASP cc_start: 0.8370 (t0) cc_final: 0.7984 (t0) REVERT: M 78 PHE cc_start: 0.9174 (m-80) cc_final: 0.8860 (m-80) outliers start: 34 outliers final: 9 residues processed: 256 average time/residue: 1.5789 time to fit residues: 433.7007 Evaluate side-chains 248 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 C residue 64 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 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 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 75 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 K 69 ASN ** L 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.098844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.063595 restraints weight = 29274.341| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.95 r_work: 0.2686 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14949 Z= 0.191 Angle : 0.570 10.935 21219 Z= 0.331 Chirality : 0.037 0.153 2427 Planarity : 0.004 0.047 1841 Dihedral : 28.753 98.459 3938 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.25 % Allowed : 17.89 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.24), residues: 1133 helix: 2.22 (0.19), residues: 679 sheet: 0.48 (0.48), residues: 119 loop : -0.20 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 42 HIS 0.004 0.001 HIS B 75 PHE 0.023 0.001 PHE K 182 TYR 0.014 0.001 TYR G 57 ARG 0.010 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 874) hydrogen bonds : angle 3.31071 ( 2273) covalent geometry : bond 0.00430 (14949) covalent geometry : angle 0.56972 (21219) *********************** 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 273 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.9081 (tttp) cc_final: 0.8827 (tttp) REVERT: A 94 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8426 (mm-30) REVERT: A 120 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.8562 (mtp) REVERT: C 62 ILE cc_start: 0.9537 (mt) cc_final: 0.9289 (tt) REVERT: C 73 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.8939 (t0) REVERT: D 90 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: E 59 GLU cc_start: 0.8953 (pm20) cc_final: 0.8619 (pm20) REVERT: E 120 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.9042 (mtt) REVERT: G 36 LYS cc_start: 0.9274 (mmpt) cc_final: 0.8930 (mmmm) REVERT: G 104 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8581 (mm110) REVERT: H 73 GLU cc_start: 0.9196 (tp30) cc_final: 0.8954 (tp30) REVERT: K 69 ASN cc_start: 0.6853 (t0) cc_final: 0.6639 (t0) REVERT: K 95 ASN cc_start: 0.9058 (t0) cc_final: 0.8828 (t0) REVERT: K 148 PHE cc_start: 0.8332 (m-80) cc_final: 0.7961 (m-80) REVERT: K 156 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8680 (ptmm) REVERT: K 225 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8369 (pm20) REVERT: L 12 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8820 (mp) REVERT: L 248 TYR cc_start: 0.8568 (p90) cc_final: 0.8254 (p90) REVERT: L 278 LYS cc_start: 0.8428 (pttt) cc_final: 0.8211 (pptt) REVERT: M 74 ASP cc_start: 0.8377 (t0) cc_final: 0.7986 (t0) REVERT: M 78 PHE cc_start: 0.9203 (m-80) cc_final: 0.8881 (m-80) REVERT: M 112 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7937 (ttp-170) outliers start: 32 outliers final: 6 residues processed: 254 average time/residue: 1.3912 time to fit residues: 382.3341 Evaluate side-chains 248 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 234 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 73 ASN 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 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 225 GLN Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 112 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 101 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 E 113 HIS K 88 HIS L 280 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.099256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.064233 restraints weight = 29342.571| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.93 r_work: 0.2696 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14949 Z= 0.173 Angle : 0.568 11.698 21219 Z= 0.328 Chirality : 0.036 0.157 2427 Planarity : 0.004 0.046 1841 Dihedral : 28.683 98.222 3938 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.66 % Allowed : 18.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.24), residues: 1133 helix: 2.31 (0.19), residues: 679 sheet: 0.36 (0.48), residues: 117 loop : -0.13 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 42 HIS 0.004 0.001 HIS B 75 PHE 0.023 0.001 PHE K 182 TYR 0.020 0.001 TYR K 195 ARG 0.009 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 874) hydrogen bonds : angle 3.29394 ( 2273) covalent geometry : bond 0.00388 (14949) covalent geometry : angle 0.56849 (21219) *********************** 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 275 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8424 (mm-30) REVERT: A 120 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8549 (mtp) REVERT: A 133 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: C 62 ILE cc_start: 0.9546 (mt) cc_final: 0.9298 (tt) REVERT: C 64 GLU cc_start: 0.8974 (tt0) cc_final: 0.8664 (tp30) REVERT: C 73 ASN cc_start: 0.9280 (OUTLIER) cc_final: 0.8895 (t0) REVERT: D 90 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: E 59 GLU cc_start: 0.8951 (pm20) cc_final: 0.8596 (pm20) REVERT: G 36 LYS cc_start: 0.9264 (mmpt) cc_final: 0.8909 (mmmm) REVERT: G 104 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8598 (mm110) REVERT: H 73 GLU cc_start: 0.9216 (tp30) cc_final: 0.8974 (tp30) REVERT: K 95 ASN cc_start: 0.9043 (t0) cc_final: 0.8826 (t0) REVERT: K 148 PHE cc_start: 0.8386 (m-80) cc_final: 0.8035 (m-80) REVERT: K 156 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8730 (ptmm) REVERT: L 12 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8807 (mp) REVERT: L 248 TYR cc_start: 0.8593 (p90) cc_final: 0.8274 (p90) REVERT: M 78 PHE cc_start: 0.9238 (m-80) cc_final: 0.8905 (m-80) outliers start: 36 outliers final: 12 residues processed: 258 average time/residue: 1.4073 time to fit residues: 392.9083 Evaluate side-chains 254 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 236 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 C residue 73 ASN 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 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 225 GLN Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain M residue 21 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 12 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 H 60 ASN K 69 ASN K 88 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.099684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.064726 restraints weight = 29530.355| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.94 r_work: 0.2708 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14949 Z= 0.165 Angle : 0.565 12.064 21219 Z= 0.327 Chirality : 0.036 0.181 2427 Planarity : 0.004 0.045 1841 Dihedral : 28.549 98.062 3938 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.95 % Allowed : 19.92 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.24), residues: 1133 helix: 2.36 (0.19), residues: 679 sheet: 0.16 (0.47), residues: 122 loop : -0.10 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 42 HIS 0.004 0.001 HIS B 75 PHE 0.023 0.001 PHE K 182 TYR 0.017 0.001 TYR K 195 ARG 0.009 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 874) hydrogen bonds : angle 3.26844 ( 2273) covalent geometry : bond 0.00369 (14949) covalent geometry : angle 0.56512 (21219) *********************** 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 271 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8745 (mm-30) REVERT: A 133 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: C 62 ILE cc_start: 0.9539 (mt) cc_final: 0.9293 (tt) REVERT: C 64 GLU cc_start: 0.8961 (tt0) cc_final: 0.8637 (tp30) REVERT: C 73 ASN cc_start: 0.9247 (t0) cc_final: 0.8848 (t160) REVERT: D 90 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8452 (mp0) REVERT: E 59 GLU cc_start: 0.8947 (pm20) cc_final: 0.8571 (pm20) REVERT: H 73 GLU cc_start: 0.9173 (tp30) cc_final: 0.8908 (tp30) REVERT: K 95 ASN cc_start: 0.9036 (t0) cc_final: 0.8824 (t0) REVERT: K 148 PHE cc_start: 0.8433 (m-80) cc_final: 0.8074 (m-80) REVERT: K 156 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8687 (ptmm) REVERT: K 220 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.6889 (mtp85) REVERT: L 12 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8823 (mp) REVERT: L 248 TYR cc_start: 0.8560 (p90) cc_final: 0.8231 (p90) REVERT: M 74 ASP cc_start: 0.8383 (t0) cc_final: 0.8016 (t0) REVERT: M 78 PHE cc_start: 0.9247 (m-80) cc_final: 0.8919 (m-80) REVERT: M 112 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7933 (ttp-170) outliers start: 29 outliers final: 11 residues processed: 256 average time/residue: 1.4823 time to fit residues: 411.2841 Evaluate side-chains 256 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 239 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 53 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU 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 214 LEU Chi-restraints excluded: chain K residue 220 ARG 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 68 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 112 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 92 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 121 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 K 69 ASN K 88 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.100373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.065598 restraints weight = 29476.079| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.94 r_work: 0.2725 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2953 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= 0.146 Angle : 0.577 12.250 21219 Z= 0.330 Chirality : 0.036 0.175 2427 Planarity : 0.004 0.058 1841 Dihedral : 28.469 98.101 3938 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.95 % Allowed : 20.93 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.24), residues: 1133 helix: 2.41 (0.19), residues: 680 sheet: 0.38 (0.48), residues: 117 loop : -0.16 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 42 HIS 0.003 0.001 HIS B 75 PHE 0.016 0.001 PHE K 155 TYR 0.010 0.001 TYR C 57 ARG 0.010 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 874) hydrogen bonds : angle 3.25952 ( 2273) covalent geometry : bond 0.00321 (14949) covalent geometry : angle 0.57696 (21219) *********************** 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 272 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8516 (mm-30) REVERT: C 62 ILE cc_start: 0.9515 (mt) cc_final: 0.9287 (tt) REVERT: C 64 GLU cc_start: 0.8941 (tt0) cc_final: 0.8611 (tp30) REVERT: C 73 ASN cc_start: 0.9262 (t0) cc_final: 0.8846 (t0) REVERT: D 90 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8430 (mp0) REVERT: E 59 GLU cc_start: 0.8913 (pm20) cc_final: 0.8389 (pm20) REVERT: F 88 TYR cc_start: 0.9341 (m-10) cc_final: 0.9131 (m-10) REVERT: G 104 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8650 (mm-40) REVERT: H 73 GLU cc_start: 0.9168 (tp30) cc_final: 0.8942 (tp30) REVERT: K 95 ASN cc_start: 0.9028 (t0) cc_final: 0.8819 (t0) REVERT: K 148 PHE cc_start: 0.8448 (m-80) cc_final: 0.8092 (m-80) REVERT: L 12 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8833 (mp) REVERT: L 248 TYR cc_start: 0.8537 (p90) cc_final: 0.8197 (p90) REVERT: M 38 MET cc_start: 0.8899 (mmp) cc_final: 0.8289 (pp-130) REVERT: M 78 PHE cc_start: 0.9239 (m-80) cc_final: 0.8949 (m-80) REVERT: M 112 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7920 (ttp-170) outliers start: 29 outliers final: 11 residues processed: 259 average time/residue: 1.4567 time to fit residues: 408.1266 Evaluate side-chains 252 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 52 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 170 ILE 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 68 THR Chi-restraints excluded: chain M residue 83 CYS Chi-restraints excluded: chain M residue 112 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.100896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.066046 restraints weight = 29267.039| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.94 r_work: 0.2752 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14949 Z= 0.149 Angle : 0.582 12.699 21219 Z= 0.332 Chirality : 0.036 0.183 2427 Planarity : 0.004 0.045 1841 Dihedral : 28.344 97.252 3938 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.44 % Allowed : 21.04 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.25), residues: 1133 helix: 2.46 (0.19), residues: 677 sheet: 0.40 (0.49), residues: 117 loop : -0.12 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 42 HIS 0.003 0.000 HIS F 75 PHE 0.014 0.001 PHE K 155 TYR 0.019 0.001 TYR K 195 ARG 0.010 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 874) hydrogen bonds : angle 3.24808 ( 2273) covalent geometry : bond 0.00331 (14949) covalent geometry : angle 0.58232 (21219) *********************** 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 269 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 245 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8357 (mm-30) REVERT: C 64 GLU cc_start: 0.8951 (tt0) cc_final: 0.8617 (tp30) REVERT: C 73 ASN cc_start: 0.9276 (t0) cc_final: 0.8853 (t0) REVERT: D 90 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8412 (mp0) REVERT: E 59 GLU cc_start: 0.8826 (pm20) cc_final: 0.8398 (pm20) REVERT: G 36 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8942 (mmmm) REVERT: G 104 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8622 (mm110) REVERT: H 73 GLU cc_start: 0.9177 (tp30) cc_final: 0.8954 (tp30) REVERT: K 148 PHE cc_start: 0.8476 (m-80) cc_final: 0.8162 (m-80) REVERT: L 12 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8857 (mp) REVERT: M 78 PHE cc_start: 0.9209 (m-80) cc_final: 0.8931 (m-80) REVERT: M 112 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7945 (ttp-170) outliers start: 24 outliers final: 12 residues processed: 258 average time/residue: 1.6934 time to fit residues: 471.8262 Evaluate side-chains 253 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 238 time to evaluate : 1.598 ------------------------------------------------------------------------------- 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 90 GLU 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 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 68 THR Chi-restraints excluded: chain M residue 112 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 108 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 116 optimal weight: 0.0970 chunk 107 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 106 optimal weight: 20.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 K 88 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.097956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.062820 restraints weight = 29325.656| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.93 r_work: 0.2663 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14949 Z= 0.229 Angle : 0.617 12.383 21219 Z= 0.350 Chirality : 0.039 0.198 2427 Planarity : 0.004 0.043 1841 Dihedral : 28.669 98.202 3938 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.24 % Allowed : 22.05 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.25), residues: 1133 helix: 2.28 (0.19), residues: 680 sheet: 0.09 (0.48), residues: 122 loop : -0.10 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP L 42 HIS 0.005 0.001 HIS B 75 PHE 0.013 0.001 PHE K 155 TYR 0.013 0.001 TYR D 37 ARG 0.014 0.001 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 874) hydrogen bonds : angle 3.35102 ( 2273) covalent geometry : bond 0.00525 (14949) covalent geometry : angle 0.61693 (21219) *********************** 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: 22 poor density : 231 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8458 (mm-30) REVERT: C 62 ILE cc_start: 0.9557 (mt) cc_final: 0.9315 (tt) REVERT: C 64 GLU cc_start: 0.9015 (tt0) cc_final: 0.8679 (tp30) REVERT: C 73 ASN cc_start: 0.9204 (t0) cc_final: 0.8820 (t0) REVERT: D 90 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8434 (mp0) REVERT: E 59 GLU cc_start: 0.8863 (pm20) cc_final: 0.8469 (pm20) REVERT: F 85 ASP cc_start: 0.9215 (m-30) cc_final: 0.8970 (m-30) REVERT: G 36 LYS cc_start: 0.9201 (mmmt) cc_final: 0.8940 (mmmm) REVERT: G 104 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8688 (mm110) REVERT: H 73 GLU cc_start: 0.9170 (tp30) cc_final: 0.8924 (tp30) REVERT: K 148 PHE cc_start: 0.8429 (m-80) cc_final: 0.8122 (m-80) REVERT: L 12 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8910 (mp) REVERT: L 248 TYR cc_start: 0.8591 (p90) cc_final: 0.8244 (p90) REVERT: M 74 ASP cc_start: 0.8348 (t0) cc_final: 0.8038 (t0) REVERT: M 78 PHE cc_start: 0.9230 (m-80) cc_final: 0.8928 (m-80) REVERT: M 112 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7929 (ttp-170) outliers start: 22 outliers final: 13 residues processed: 243 average time/residue: 1.5234 time to fit residues: 401.4019 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 : 1.406 ------------------------------------------------------------------------------- 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 D residue 90 GLU Chi-restraints excluded: chain F residue 49 LEU 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 225 GLN Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 112 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 112 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 39 optimal weight: 0.2980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.098767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.063553 restraints weight = 29086.236| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.93 r_work: 0.2688 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14949 Z= 0.171 Angle : 0.613 14.439 21219 Z= 0.347 Chirality : 0.038 0.189 2427 Planarity : 0.004 0.056 1841 Dihedral : 28.631 98.813 3938 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.73 % Allowed : 22.15 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.25), residues: 1133 helix: 2.25 (0.19), residues: 680 sheet: 0.26 (0.50), residues: 117 loop : -0.17 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP L 42 HIS 0.004 0.001 HIS K 88 PHE 0.021 0.001 PHE K 182 TYR 0.037 0.002 TYR F 88 ARG 0.010 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 874) hydrogen bonds : angle 3.31560 ( 2273) covalent geometry : bond 0.00384 (14949) covalent geometry : angle 0.61328 (21219) ********************** 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 254 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 237 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8534 (mm-30) REVERT: B 23 ARG cc_start: 0.8350 (ptp-110) cc_final: 0.8146 (mtm110) REVERT: C 62 ILE cc_start: 0.9552 (mt) cc_final: 0.9325 (tt) REVERT: C 64 GLU cc_start: 0.8991 (tt0) cc_final: 0.8655 (tp30) REVERT: C 73 ASN cc_start: 0.9203 (t0) cc_final: 0.8824 (t0) REVERT: D 90 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8440 (mp0) REVERT: E 59 GLU cc_start: 0.8876 (pm20) cc_final: 0.8457 (pm20) REVERT: F 85 ASP cc_start: 0.9214 (m-30) cc_final: 0.8962 (m-30) REVERT: G 36 LYS cc_start: 0.9193 (mmmt) cc_final: 0.8930 (mmmm) REVERT: G 104 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8671 (mm-40) REVERT: H 73 GLU cc_start: 0.9163 (tp30) cc_final: 0.8895 (tp30) REVERT: K 148 PHE cc_start: 0.8429 (m-80) cc_final: 0.8102 (m-80) REVERT: L 12 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8900 (mp) REVERT: M 78 PHE cc_start: 0.9217 (m-80) cc_final: 0.8909 (m-80) REVERT: M 84 GLN cc_start: 0.8666 (tt0) cc_final: 0.8294 (pt0) REVERT: M 112 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7933 (ttp-170) outliers start: 17 outliers final: 13 residues processed: 246 average time/residue: 1.8695 time to fit residues: 497.3211 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 : 1.779 ------------------------------------------------------------------------------- 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 D residue 90 GLU Chi-restraints excluded: chain F residue 49 LEU 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 225 GLN Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain M residue 21 ASP Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 112 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 126 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.098544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.063410 restraints weight = 29561.198| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.93 r_work: 0.2678 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14949 Z= 0.200 Angle : 0.609 14.064 21219 Z= 0.345 Chirality : 0.038 0.190 2427 Planarity : 0.004 0.044 1841 Dihedral : 28.557 99.202 3938 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.83 % Allowed : 22.76 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.25), residues: 1133 helix: 2.27 (0.19), residues: 680 sheet: 0.23 (0.49), residues: 119 loop : -0.19 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP L 42 HIS 0.005 0.001 HIS B 75 PHE 0.025 0.001 PHE K 182 TYR 0.039 0.002 TYR F 88 ARG 0.009 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 874) hydrogen bonds : angle 3.31752 ( 2273) covalent geometry : bond 0.00453 (14949) covalent geometry : angle 0.60891 (21219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13170.94 seconds wall clock time: 230 minutes 33.11 seconds (13833.11 seconds total)