Starting phenix.real_space_refine on Sun Dec 10 10:10:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oha_12898/12_2023/7oha_12898.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oha_12898/12_2023/7oha_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_12898/12_2023/7oha_12898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oha_12898/12_2023/7oha_12898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oha_12898/12_2023/7oha_12898.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oha_12898/12_2023/7oha_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-1.21rc1-5172/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: 7.46, per 1000 atoms: 0.52 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: 6.69 Conformation dependent library (CDL) restraints added in 1.9 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: 6.18 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: 5.79 Time building geometry restraints manager: 7.03 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: 0.360 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: 2.430 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 44.250 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.000 ------------------------------------------------------------------------------- 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 : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 1.4816 time to fit residues: 469.3729 Evaluate side-chains 257 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6718 ------------------------------------------------------------------------------- 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: 0.6980 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: 20.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN 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: 0.8416 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14949 Z= 0.244 Angle : 0.581 11.266 21219 Z= 0.339 Chirality : 0.037 0.162 2427 Planarity : 0.004 0.059 1841 Dihedral : 29.093 95.823 3938 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.03 % Allowed : 14.84 % Favored : 83.13 % 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: 1.59 (0.24), residues: 1133 helix: 1.92 (0.19), residues: 677 sheet: 0.52 (0.46), residues: 117 loop : -0.47 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 42 HIS 0.004 0.001 HIS B 75 PHE 0.023 0.002 PHE K 182 TYR 0.018 0.002 TYR L 248 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 273 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 253 time to evaluate : 1.153 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 5 residues processed: 261 average time/residue: 1.4785 time to fit residues: 416.3887 Evaluate side-chains 235 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 230 time to evaluate : 1.213 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.1197 time to fit residues: 2.0574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 131 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 81 ASN K 69 ASN ** L 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14949 Z= 0.212 Angle : 0.563 10.729 21219 Z= 0.327 Chirality : 0.036 0.146 2427 Planarity : 0.004 0.060 1841 Dihedral : 28.822 96.520 3938 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.64 % Allowed : 17.48 % Favored : 79.88 % 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: 2.27 (0.19), residues: 674 sheet: 0.63 (0.46), residues: 118 loop : -0.38 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 42 HIS 0.003 0.001 HIS B 75 PHE 0.016 0.001 PHE K 182 TYR 0.016 0.001 TYR K 195 ARG 0.010 0.000 ARG K 79 *********************** 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 278 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 252 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 8 residues processed: 265 average time/residue: 1.5778 time to fit residues: 449.7843 Evaluate side-chains 246 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 238 time to evaluate : 1.263 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.1731 time to fit residues: 2.4431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- 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 ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8516 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 14949 Z= 0.506 Angle : 0.668 10.467 21219 Z= 0.379 Chirality : 0.045 0.144 2427 Planarity : 0.005 0.049 1841 Dihedral : 29.350 99.620 3938 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.66 % Allowed : 17.38 % Favored : 78.96 % 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: 1.98 (0.19), residues: 680 sheet: 0.64 (0.48), residues: 119 loop : -0.31 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP L 42 HIS 0.005 0.001 HIS A 113 PHE 0.024 0.002 PHE G 25 TYR 0.021 0.002 TYR F 88 ARG 0.008 0.001 ARG K 171 *********************** 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 fitting. rotamer outliers: 36 poor density : 237 time to evaluate : 1.414 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 15 residues processed: 254 average time/residue: 1.5651 time to fit residues: 427.9152 Evaluate side-chains 242 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 227 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.4543 time to fit residues: 4.4689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14949 Z= 0.204 Angle : 0.600 11.802 21219 Z= 0.343 Chirality : 0.038 0.198 2427 Planarity : 0.005 0.077 1841 Dihedral : 29.161 102.510 3938 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.95 % Allowed : 19.21 % Favored : 77.85 % 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: 1.84 (0.24), residues: 1133 helix: 2.10 (0.19), residues: 680 sheet: 0.37 (0.48), residues: 119 loop : -0.23 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 42 HIS 0.002 0.001 HIS F 75 PHE 0.020 0.002 PHE K 190 TYR 0.023 0.001 TYR K 195 ARG 0.015 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 275 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 246 time to evaluate : 1.350 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 10 residues processed: 260 average time/residue: 1.5012 time to fit residues: 421.1919 Evaluate side-chains 251 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 241 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.4580 time to fit residues: 3.3121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 C 104 GLN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 69 ASN ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14949 Z= 0.274 Angle : 0.596 12.309 21219 Z= 0.342 Chirality : 0.038 0.165 2427 Planarity : 0.004 0.044 1841 Dihedral : 28.809 102.574 3938 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.85 % Allowed : 20.22 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.23 (0.19), residues: 679 sheet: 0.21 (0.47), residues: 119 loop : -0.14 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 42 HIS 0.003 0.001 HIS F 75 PHE 0.020 0.002 PHE K 182 TYR 0.012 0.001 TYR G 57 ARG 0.008 0.001 ARG D 83 *********************** 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 262 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 234 time to evaluate : 1.180 Fit side-chains outliers start: 28 outliers final: 13 residues processed: 248 average time/residue: 1.4797 time to fit residues: 396.8927 Evaluate side-chains 244 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 231 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 6 residues processed: 7 average time/residue: 0.6474 time to fit residues: 6.8423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN H 60 ASN K 69 ASN K 144 GLN ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14949 Z= 0.362 Angle : 0.616 12.619 21219 Z= 0.351 Chirality : 0.040 0.183 2427 Planarity : 0.004 0.041 1841 Dihedral : 28.925 105.121 3938 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % 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: 1.90 (0.25), residues: 1133 helix: 2.18 (0.19), residues: 680 sheet: 0.00 (0.47), residues: 124 loop : -0.13 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP L 42 HIS 0.003 0.001 HIS F 75 PHE 0.015 0.002 PHE K 155 TYR 0.029 0.002 TYR K 195 ARG 0.007 0.001 ARG D 83 *********************** 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 247 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 223 time to evaluate : 1.313 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 235 average time/residue: 1.5015 time to fit residues: 381.1708 Evaluate side-chains 233 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 222 time to evaluate : 1.321 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.8181 time to fit residues: 4.4475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- 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 C 104 GLN K 69 ASN ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14949 Z= 0.352 Angle : 0.614 13.194 21219 Z= 0.350 Chirality : 0.040 0.179 2427 Planarity : 0.004 0.041 1841 Dihedral : 28.866 108.050 3938 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.42 % Allowed : 21.95 % Favored : 76.63 % 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: 1.86 (0.25), residues: 1133 helix: 2.16 (0.19), residues: 680 sheet: -0.09 (0.47), residues: 124 loop : -0.14 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP L 42 HIS 0.003 0.001 HIS F 75 PHE 0.024 0.002 PHE K 190 TYR 0.018 0.002 TYR H 118 ARG 0.013 0.001 ARG B 23 *********************** 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 242 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 228 time to evaluate : 1.314 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 236 average time/residue: 1.4525 time to fit residues: 371.8467 Evaluate side-chains 240 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 227 time to evaluate : 1.354 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.7425 time to fit residues: 6.1697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 C 104 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 69 ASN ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 14949 Z= 0.519 Angle : 0.679 13.137 21219 Z= 0.382 Chirality : 0.045 0.190 2427 Planarity : 0.005 0.042 1841 Dihedral : 29.253 114.393 3938 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.44 % Allowed : 21.34 % Favored : 76.22 % 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: 1.60 (0.25), residues: 1133 helix: 1.97 (0.19), residues: 680 sheet: -0.27 (0.47), residues: 124 loop : -0.25 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP L 42 HIS 0.005 0.001 HIS H 79 PHE 0.031 0.003 PHE K 190 TYR 0.038 0.002 TYR F 88 ARG 0.006 0.001 ARG D 83 *********************** 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 248 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 224 time to evaluate : 1.257 Fit side-chains outliers start: 24 outliers final: 13 residues processed: 234 average time/residue: 1.5542 time to fit residues: 392.6065 Evaluate side-chains 237 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 224 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.5678 time to fit residues: 5.6639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 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 C 73 ASN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 69 ASN K 144 GLN ** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14949 Z= 0.274 Angle : 0.633 14.809 21219 Z= 0.360 Chirality : 0.039 0.142 2427 Planarity : 0.005 0.105 1841 Dihedral : 29.236 116.456 3938 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.02 % Allowed : 23.48 % Favored : 75.51 % 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: 1.58 (0.25), residues: 1133 helix: 1.98 (0.19), residues: 680 sheet: -0.39 (0.47), residues: 124 loop : -0.26 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP L 42 HIS 0.003 0.001 HIS F 75 PHE 0.027 0.002 PHE K 190 TYR 0.041 0.002 TYR F 88 ARG 0.014 0.001 ARG B 23 ********************** 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 241 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 231 time to evaluate : 1.407 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 238 average time/residue: 1.4694 time to fit residues: 378.7789 Evaluate side-chains 238 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 229 time to evaluate : 1.228 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 1.4908 time to fit residues: 4.7578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.0370 chunk 98 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 104 GLN K 69 ASN ** K 225 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 = 0.3565 r_free = 0.3565 target = 0.098365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.063717 restraints weight = 29214.285| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.92 r_work: 0.2688 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14949 Z= 0.216 Angle : 0.597 14.239 21219 Z= 0.339 Chirality : 0.037 0.141 2427 Planarity : 0.004 0.040 1841 Dihedral : 28.575 115.035 3938 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.81 % Allowed : 23.88 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.85 (0.25), residues: 1133 helix: 2.24 (0.19), residues: 680 sheet: -0.27 (0.50), residues: 118 loop : -0.29 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 42 HIS 0.003 0.001 HIS F 75 PHE 0.021 0.002 PHE K 190 TYR 0.035 0.002 TYR F 88 ARG 0.006 0.000 ARG D 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6152.55 seconds wall clock time: 112 minutes 10.45 seconds (6730.45 seconds total)