Starting phenix.real_space_refine on Fri Feb 16 03:03:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oha_12898/02_2024/7oha_12898.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oha_12898/02_2024/7oha_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oha_12898/02_2024/7oha_12898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oha_12898/02_2024/7oha_12898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oha_12898/02_2024/7oha_12898.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oha_12898/02_2024/7oha_12898.pdb" } 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 Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "L TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 21": "OD1" <-> "OD2" Residue "M GLU 50": "OE1" <-> "OE2" Residue "M ASP 109": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.70, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 6.67 Conformation dependent library (CDL) restraints added in 1.8 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: 6.69 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: 6.35 Time building geometry restraints manager: 7.00 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: 96.08 - 103.71: 696 103.71 - 111.33: 7136 111.33 - 118.95: 5356 118.95 - 126.57: 7287 126.57 - 134.19: 744 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 2.440 nonbonded pdb=" OG SER K 183 " pdb=" O ILE K 194 " model vdw 2.273 2.440 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.286 2.440 nonbonded pdb=" OH TYR M 7 " pdb=" O ASN M 117 " model vdw 2.296 2.440 nonbonded pdb=" NH1 ARG G 42 " pdb=" OG1 THR H 85 " model vdw 2.322 2.520 ... (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 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.460 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 46.330 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.180 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:12.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.280 ------------------------------------------------------------------------------- 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= 0.305 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.191 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: 1.4482 time to fit residues: 458.8483 Evaluate side-chains 257 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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: 8.9990 chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 H 60 ASN H 64 ASN ** L 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14949 Z= 0.265 Angle : 0.587 11.169 21219 Z= 0.342 Chirality : 0.038 0.182 2427 Planarity : 0.004 0.058 1841 Dihedral : 29.136 96.032 3938 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.13 % Allowed : 14.53 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.55 (0.24), residues: 1133 helix: 1.88 (0.19), residues: 677 sheet: 0.52 (0.46), residues: 117 loop : -0.48 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 42 HIS 0.004 0.001 HIS F 75 PHE 0.023 0.002 PHE K 182 TYR 0.013 0.002 TYR F 88 ARG 0.007 0.000 ARG D 83 *********************** 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 272 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 251 time to evaluate : 1.230 Fit side-chains REVERT: A 58 THR cc_start: 0.9489 (p) cc_final: 0.9115 (t) REVERT: A 94 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7287 (mm-30) REVERT: A 133 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: C 95 LYS cc_start: 0.9089 (ttpp) cc_final: 0.8849 (ttpp) REVERT: D 56 MET cc_start: 0.9161 (tpp) cc_final: 0.8914 (tpp) REVERT: E 42 ARG cc_start: 0.8500 (mtp-110) cc_final: 0.8270 (mtp-110) REVERT: E 59 GLU cc_start: 0.8410 (pm20) cc_final: 0.8205 (pm20) REVERT: E 96 SER cc_start: 0.9285 (m) cc_final: 0.9078 (m) REVERT: E 120 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.7954 (mtm) REVERT: F 88 TYR cc_start: 0.9030 (m-10) cc_final: 0.8826 (m-10) REVERT: G 36 LYS cc_start: 0.8962 (mmpt) cc_final: 0.8661 (mmmm) REVERT: G 104 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8122 (mm110) REVERT: K 95 ASN cc_start: 0.9017 (t0) cc_final: 0.8764 (t0) REVERT: K 189 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8671 (tt) REVERT: L 248 TYR cc_start: 0.8105 (p90) cc_final: 0.7674 (p90) REVERT: L 258 TRP cc_start: 0.8106 (m100) cc_final: 0.7814 (t-100) REVERT: M 74 ASP cc_start: 0.7813 (t0) cc_final: 0.7453 (t0) outliers start: 21 outliers final: 5 residues processed: 258 average time/residue: 1.5369 time to fit residues: 427.1194 Evaluate side-chains 236 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 228 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 37 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 121 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 108 optimal weight: 0.0470 chunk 120 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.3080 ------------------------------------------------------------------------------- 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 D 81 ASN K 69 ASN ** L 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14949 Z= 0.197 Angle : 0.551 10.692 21219 Z= 0.322 Chirality : 0.036 0.146 2427 Planarity : 0.004 0.068 1841 Dihedral : 28.744 96.763 3938 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.34 % Allowed : 17.38 % 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: 1.98 (0.24), residues: 1133 helix: 2.26 (0.19), residues: 677 sheet: 0.68 (0.46), residues: 118 loop : -0.39 (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 0.016 0.001 PHE K 182 TYR 0.013 0.001 TYR G 57 ARG 0.008 0.000 ARG D 83 *********************** 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 279 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 256 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8797 (tttp) cc_final: 0.8563 (tttp) REVERT: A 94 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7199 (mm-30) REVERT: C 95 LYS cc_start: 0.9086 (ttpp) cc_final: 0.8867 (ttpp) REVERT: D 56 MET cc_start: 0.9157 (tpp) cc_final: 0.8868 (tpp) REVERT: E 59 GLU cc_start: 0.8473 (pm20) cc_final: 0.8196 (pm20) REVERT: E 120 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8020 (mtm) REVERT: G 36 LYS cc_start: 0.9003 (mmpt) cc_final: 0.8704 (mmmm) REVERT: G 104 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8139 (mm110) REVERT: K 95 ASN cc_start: 0.9055 (t0) cc_final: 0.8839 (t0) REVERT: K 141 ARG cc_start: 0.8582 (mmm-85) cc_final: 0.8364 (ttp80) REVERT: K 148 PHE cc_start: 0.8782 (m-80) cc_final: 0.8377 (m-80) REVERT: K 171 ARG cc_start: 0.7855 (mpp80) cc_final: 0.7096 (mpp80) REVERT: K 189 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8567 (tt) REVERT: K 225 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8240 (pm20) REVERT: L 248 TYR cc_start: 0.8262 (p90) cc_final: 0.7836 (p90) REVERT: L 258 TRP cc_start: 0.8116 (m100) cc_final: 0.7746 (t-100) REVERT: M 21 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8648 (p0) REVERT: M 74 ASP cc_start: 0.7916 (t0) cc_final: 0.7517 (t0) outliers start: 23 outliers final: 6 residues processed: 267 average time/residue: 1.5105 time to fit residues: 434.3158 Evaluate side-chains 252 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 242 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 85 ASP 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 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 120 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 129 optimal weight: 0.0770 chunk 115 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 75 HIS C 31 HIS C 73 ASN H 46 HIS H 60 ASN K 69 ASN K 91 ASN L 280 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14949 Z= 0.313 Angle : 0.587 10.691 21219 Z= 0.338 Chirality : 0.039 0.142 2427 Planarity : 0.004 0.046 1841 Dihedral : 28.950 97.794 3938 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.66 % Allowed : 17.68 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.24), residues: 1133 helix: 2.22 (0.19), residues: 679 sheet: 0.67 (0.48), residues: 119 loop : -0.27 (0.31), residues: 335 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 0.021 0.002 PHE K 182 TYR 0.011 0.001 TYR F 51 ARG 0.008 0.001 ARG D 83 *********************** 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 276 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 240 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: C 64 GLU cc_start: 0.8151 (tt0) cc_final: 0.7909 (tp30) REVERT: C 73 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8805 (t0) REVERT: D 56 MET cc_start: 0.9180 (tpp) cc_final: 0.8911 (tpp) REVERT: E 59 GLU cc_start: 0.8558 (pm20) cc_final: 0.8286 (pm20) REVERT: E 120 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8597 (mtt) REVERT: F 88 TYR cc_start: 0.9127 (m-10) cc_final: 0.8913 (m-10) REVERT: G 36 LYS cc_start: 0.9004 (mmpt) cc_final: 0.8674 (mmmm) REVERT: H 73 GLU cc_start: 0.8341 (tp30) cc_final: 0.8133 (tp30) REVERT: K 90 ARG cc_start: 0.8171 (ptt180) cc_final: 0.7921 (ptt180) REVERT: K 95 ASN cc_start: 0.9029 (t0) cc_final: 0.8805 (t0) REVERT: K 148 PHE cc_start: 0.8825 (m-80) cc_final: 0.8400 (m-80) REVERT: K 171 ARG cc_start: 0.7997 (mpp80) cc_final: 0.7349 (mpp80) REVERT: K 225 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8211 (pm20) REVERT: L 12 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8925 (mp) REVERT: M 74 ASP cc_start: 0.7887 (t0) cc_final: 0.7496 (t0) outliers start: 36 outliers final: 15 residues processed: 255 average time/residue: 1.5290 time to fit residues: 419.7632 Evaluate side-chains 255 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 235 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 54 LYS 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 68 THR Chi-restraints excluded: chain M residue 83 CYS Chi-restraints excluded: chain M residue 108 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 0 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 K 88 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14949 Z= 0.203 Angle : 0.560 11.875 21219 Z= 0.323 Chirality : 0.036 0.174 2427 Planarity : 0.004 0.065 1841 Dihedral : 28.599 98.204 3938 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.85 % Allowed : 19.82 % Favored : 77.34 % 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: 2.42 (0.19), residues: 675 sheet: 0.55 (0.48), residues: 119 loop : -0.20 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 42 HIS 0.003 0.001 HIS B 75 PHE 0.020 0.002 PHE K 152 TYR 0.011 0.001 TYR C 57 ARG 0.014 0.001 ARG K 79 *********************** 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 274 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 246 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8668 (pm20) cc_final: 0.8367 (pm20) REVERT: A 133 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: C 64 GLU cc_start: 0.8092 (tt0) cc_final: 0.7850 (tp30) REVERT: C 73 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8668 (t160) REVERT: D 56 MET cc_start: 0.9180 (tpp) cc_final: 0.8930 (tpp) REVERT: E 59 GLU cc_start: 0.8578 (pm20) cc_final: 0.8344 (pm20) REVERT: E 120 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8503 (mtt) REVERT: H 73 GLU cc_start: 0.8259 (tp30) cc_final: 0.8025 (tp30) REVERT: K 90 ARG cc_start: 0.8118 (ptt180) cc_final: 0.7810 (ptt180) REVERT: K 148 PHE cc_start: 0.8898 (m-80) cc_final: 0.8460 (m-80) REVERT: K 171 ARG cc_start: 0.8090 (mpp80) cc_final: 0.7521 (mpp80) REVERT: K 238 ARG cc_start: 0.7998 (ttt90) cc_final: 0.7733 (ttt90) REVERT: L 12 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8906 (mp) outliers start: 28 outliers final: 12 residues processed: 260 average time/residue: 1.5465 time to fit residues: 433.1055 Evaluate side-chains 259 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 243 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR 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 73 ASN Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 120 MET 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 108 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 129 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 E 113 HIS H 60 ASN K 69 ASN K 88 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14949 Z= 0.194 Angle : 0.551 12.231 21219 Z= 0.319 Chirality : 0.036 0.177 2427 Planarity : 0.004 0.046 1841 Dihedral : 28.447 98.378 3938 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.05 % Allowed : 20.53 % 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 (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: 2.27 (0.25), residues: 1133 helix: 2.48 (0.19), residues: 678 sheet: 0.42 (0.47), residues: 124 loop : -0.11 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 42 HIS 0.004 0.001 HIS B 75 PHE 0.016 0.001 PHE M 78 TYR 0.027 0.001 TYR K 195 ARG 0.007 0.000 ARG K 238 *********************** 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 280 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 250 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8671 (pm20) cc_final: 0.8371 (pm20) REVERT: A 94 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7199 (mt-10) REVERT: C 64 GLU cc_start: 0.8087 (tt0) cc_final: 0.7830 (tp30) REVERT: C 73 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8661 (t160) REVERT: D 56 MET cc_start: 0.9177 (tpp) cc_final: 0.8939 (tpp) REVERT: E 59 GLU cc_start: 0.8587 (pm20) cc_final: 0.8234 (pm20) REVERT: E 120 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8532 (mtt) REVERT: G 36 LYS cc_start: 0.8993 (mmpt) cc_final: 0.8679 (mmmm) REVERT: H 73 GLU cc_start: 0.8264 (tp30) cc_final: 0.8026 (tp30) REVERT: K 90 ARG cc_start: 0.8121 (ptt180) cc_final: 0.7850 (ptt180) REVERT: K 148 PHE cc_start: 0.8921 (m-80) cc_final: 0.8594 (m-80) REVERT: K 156 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8684 (ptmm) REVERT: K 171 ARG cc_start: 0.8130 (mpp80) cc_final: 0.7403 (mpp80) REVERT: K 220 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7997 (mtp85) REVERT: L 12 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8917 (mp) REVERT: M 84 GLN cc_start: 0.8838 (tt0) cc_final: 0.8550 (tt0) outliers start: 30 outliers final: 13 residues processed: 268 average time/residue: 1.4642 time to fit residues: 423.6327 Evaluate side-chains 265 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 247 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 120 MET 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 156 LYS Chi-restraints excluded: chain K residue 170 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 51 optimal weight: 0.1980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN K 69 ASN K 88 HIS K 144 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3104 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= 0.257 Angle : 0.580 12.715 21219 Z= 0.330 Chirality : 0.037 0.171 2427 Planarity : 0.004 0.073 1841 Dihedral : 28.507 98.755 3938 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.15 % Allowed : 21.04 % Favored : 75.81 % 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: 2.21 (0.25), residues: 1133 helix: 2.43 (0.19), residues: 679 sheet: 0.33 (0.47), residues: 124 loop : -0.10 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 42 HIS 0.003 0.001 HIS F 75 PHE 0.019 0.002 PHE K 190 TYR 0.012 0.001 TYR G 57 ARG 0.016 0.001 ARG K 79 *********************** 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 276 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 245 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8102 (tt0) cc_final: 0.7834 (tp30) REVERT: C 73 ASN cc_start: 0.8975 (t0) cc_final: 0.8643 (t160) REVERT: D 56 MET cc_start: 0.9181 (tpp) cc_final: 0.8912 (tpp) REVERT: E 59 GLU cc_start: 0.8504 (pm20) cc_final: 0.8247 (pm20) REVERT: E 120 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8543 (mtt) REVERT: G 36 LYS cc_start: 0.8991 (mmpt) cc_final: 0.8675 (mmmm) REVERT: H 73 GLU cc_start: 0.8273 (tp30) cc_final: 0.8046 (tp30) REVERT: K 90 ARG cc_start: 0.8084 (ptt180) cc_final: 0.7744 (ptt180) REVERT: K 141 ARG cc_start: 0.8776 (mmm-85) cc_final: 0.8495 (ttp80) REVERT: K 148 PHE cc_start: 0.8940 (m-80) cc_final: 0.8248 (m-80) REVERT: K 156 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8708 (ptmm) REVERT: K 195 TYR cc_start: 0.9100 (t80) cc_final: 0.8545 (t80) REVERT: K 220 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7986 (mtp85) REVERT: L 12 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8970 (mp) REVERT: M 74 ASP cc_start: 0.7882 (t0) cc_final: 0.7679 (t0) REVERT: M 112 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7283 (ttp-170) outliers start: 31 outliers final: 15 residues processed: 260 average time/residue: 1.5324 time to fit residues: 429.3925 Evaluate side-chains 263 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 243 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 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 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 112 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14949 Z= 0.261 Angle : 0.583 12.748 21219 Z= 0.332 Chirality : 0.037 0.193 2427 Planarity : 0.004 0.044 1841 Dihedral : 28.542 99.956 3938 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.74 % Allowed : 21.54 % 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: 2.20 (0.25), residues: 1133 helix: 2.41 (0.19), residues: 679 sheet: 0.29 (0.48), residues: 124 loop : -0.07 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 42 HIS 0.003 0.001 HIS F 75 PHE 0.026 0.002 PHE K 182 TYR 0.013 0.001 TYR G 57 ARG 0.008 0.001 ARG K 141 *********************** 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 271 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 244 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8101 (tp30) cc_final: 0.7894 (tt0) REVERT: A 133 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: C 64 GLU cc_start: 0.8120 (tt0) cc_final: 0.7860 (tp30) REVERT: C 73 ASN cc_start: 0.9063 (t0) cc_final: 0.8706 (t0) REVERT: D 56 MET cc_start: 0.9180 (tpp) cc_final: 0.8920 (tpp) REVERT: E 59 GLU cc_start: 0.8551 (pm20) cc_final: 0.8295 (pm20) REVERT: E 120 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8500 (mtt) REVERT: G 36 LYS cc_start: 0.8983 (mmpt) cc_final: 0.8669 (mmmm) REVERT: H 73 GLU cc_start: 0.8281 (tp30) cc_final: 0.8054 (tp30) REVERT: K 148 PHE cc_start: 0.8900 (m-80) cc_final: 0.8476 (m-80) REVERT: K 195 TYR cc_start: 0.9103 (t80) cc_final: 0.8586 (t80) REVERT: K 220 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.8031 (mtp85) REVERT: L 12 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9006 (mp) REVERT: M 74 ASP cc_start: 0.8028 (t0) cc_final: 0.7825 (t0) REVERT: M 84 GLN cc_start: 0.8679 (tt0) cc_final: 0.8247 (pt0) REVERT: M 112 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7302 (ttp-170) outliers start: 27 outliers final: 15 residues processed: 258 average time/residue: 1.6116 time to fit residues: 447.2584 Evaluate side-chains 254 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 234 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR 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 E residue 96 SER Chi-restraints excluded: chain E residue 120 MET 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 170 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 94 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14949 Z= 0.361 Angle : 0.624 13.121 21219 Z= 0.352 Chirality : 0.040 0.198 2427 Planarity : 0.005 0.072 1841 Dihedral : 28.795 102.238 3938 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.64 % Allowed : 21.75 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.04 (0.25), residues: 1133 helix: 2.27 (0.19), residues: 679 sheet: 0.29 (0.48), residues: 124 loop : -0.13 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP L 42 HIS 0.003 0.001 HIS F 75 PHE 0.023 0.002 PHE K 190 TYR 0.037 0.002 TYR F 88 ARG 0.019 0.001 ARG K 79 *********************** 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 264 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 238 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: C 64 GLU cc_start: 0.8140 (tt0) cc_final: 0.7895 (tp30) REVERT: C 73 ASN cc_start: 0.9095 (t0) cc_final: 0.8789 (t0) REVERT: E 59 GLU cc_start: 0.8577 (pm20) cc_final: 0.8292 (pm20) REVERT: E 120 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8518 (mtt) REVERT: G 36 LYS cc_start: 0.8984 (mmpt) cc_final: 0.8665 (mmmm) REVERT: H 73 GLU cc_start: 0.8279 (tp30) cc_final: 0.8039 (tp30) REVERT: K 148 PHE cc_start: 0.8899 (m-80) cc_final: 0.8562 (m-80) REVERT: K 156 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8706 (ptpp) REVERT: K 171 ARG cc_start: 0.8166 (mpp80) cc_final: 0.7483 (mpp80) REVERT: K 195 TYR cc_start: 0.9071 (t80) cc_final: 0.8655 (t80) REVERT: L 248 TYR cc_start: 0.8363 (p90) cc_final: 0.8047 (p90) REVERT: L 278 LYS cc_start: 0.8357 (pptt) cc_final: 0.8016 (pttt) REVERT: M 74 ASP cc_start: 0.7961 (t0) cc_final: 0.7586 (t0) REVERT: M 84 GLN cc_start: 0.8665 (tt0) cc_final: 0.8378 (pt0) REVERT: M 112 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7299 (ttp-170) outliers start: 26 outliers final: 14 residues processed: 251 average time/residue: 1.6124 time to fit residues: 434.3642 Evaluate side-chains 247 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 229 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR 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 62 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 120 MET 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 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 77 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 113 optimal weight: 0.6980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14949 Z= 0.306 Angle : 0.610 13.781 21219 Z= 0.344 Chirality : 0.039 0.200 2427 Planarity : 0.004 0.047 1841 Dihedral : 28.713 103.979 3938 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.13 % Allowed : 22.97 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.25), residues: 1133 helix: 2.25 (0.19), residues: 679 sheet: 0.18 (0.49), residues: 124 loop : -0.16 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP L 42 HIS 0.003 0.001 HIS F 75 PHE 0.026 0.002 PHE K 190 TYR 0.042 0.002 TYR F 88 ARG 0.012 0.001 ARG K 141 ********************** 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 253 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: C 64 GLU cc_start: 0.8122 (tt0) cc_final: 0.7879 (tp30) REVERT: C 73 ASN cc_start: 0.9086 (t0) cc_final: 0.8772 (t0) REVERT: E 59 GLU cc_start: 0.8581 (pm20) cc_final: 0.8296 (pm20) REVERT: E 120 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8481 (mtt) REVERT: G 36 LYS cc_start: 0.8975 (mmpt) cc_final: 0.8659 (mmmm) REVERT: H 73 GLU cc_start: 0.8284 (tp30) cc_final: 0.8040 (tp30) REVERT: K 148 PHE cc_start: 0.8888 (m-80) cc_final: 0.8206 (m-80) REVERT: K 156 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8710 (ptmm) REVERT: K 195 TYR cc_start: 0.9097 (t80) cc_final: 0.8660 (t80) REVERT: L 248 TYR cc_start: 0.8367 (p90) cc_final: 0.8135 (p90) REVERT: M 84 GLN cc_start: 0.8644 (tt0) cc_final: 0.8381 (pt0) REVERT: M 112 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7270 (ttp-170) outliers start: 21 outliers final: 16 residues processed: 244 average time/residue: 1.4527 time to fit residues: 383.0059 Evaluate side-chains 250 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 230 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 120 MET 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 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 32 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.098472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.063574 restraints weight = 29166.129| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.92 r_work: 0.2675 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14949 Z= 0.192 Angle : 0.599 14.386 21219 Z= 0.338 Chirality : 0.037 0.193 2427 Planarity : 0.005 0.097 1841 Dihedral : 28.707 104.579 3938 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.93 % Allowed : 23.68 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.02 (0.25), residues: 1133 helix: 2.28 (0.19), residues: 679 sheet: 0.31 (0.50), residues: 119 loop : -0.20 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP L 42 HIS 0.003 0.000 HIS F 75 PHE 0.026 0.002 PHE K 190 TYR 0.040 0.002 TYR F 88 ARG 0.014 0.001 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6376.78 seconds wall clock time: 114 minutes 9.43 seconds (6849.43 seconds total)