Starting phenix.real_space_refine on Thu Aug 6 02:24:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r7n_18984/08_2026/8r7n_18984.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r7n_18984/08_2026/8r7n_18984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r7n_18984/08_2026/8r7n_18984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r7n_18984/08_2026/8r7n_18984.map" model { file = "/net/cci-nas-00/data/ceres_data/8r7n_18984/08_2026/8r7n_18984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r7n_18984/08_2026/8r7n_18984.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 114 5.49 5 S 64 5.16 5 C 7819 2.51 5 N 2381 2.21 5 O 2793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13171 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2432 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 15, 'rna3p_pur': 49, 'rna3p_pyr': 41} Link IDs: {'rna2p': 24, 'rna3p': 89} Chain breaks: 2 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1032 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "C" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1261 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "D" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1829 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain: "E" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 371 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain: "F" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1730 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 10, 'TRANS': 201} Chain breaks: 1 Chain: "h" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 641 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "i" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 764 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "j" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 637 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "k" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 692 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "l" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 638 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "m" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "n" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 568 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 3.03, per 1000 atoms: 0.23 Number of scatterers: 13171 At special positions: 0 Unit cell: (106.58, 103.66, 205.86, 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 64 16.00 P 114 15.00 O 2793 8.00 N 2381 7.00 C 7819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 485.8 milliseconds 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2492 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 11 sheets defined 43.6% alpha, 22.3% beta 37 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'B' and resid 3 through 13 removed outlier: 3.727A pdb=" N GLY B 7 " --> pdb=" O VAL B 3 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN B 13 " --> pdb=" O ALA B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.806A pdb=" N CYS B 18 " --> pdb=" O PRO B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.740A pdb=" N VAL B 29 " --> pdb=" O THR B 25 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 82 removed outlier: 3.681A pdb=" N LEU B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'C' and resid 12 through 17 removed outlier: 4.148A pdb=" N GLY C 17 " --> pdb=" O PRO C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 37 removed outlier: 3.639A pdb=" N ALA C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 63 through 72 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.898A pdb=" N VAL C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.781A pdb=" N GLY C 151 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 198 Processing helix chain 'D' and resid 201 through 228 Proline residue: D 214 - end of helix Proline residue: D 225 - end of helix removed outlier: 3.582A pdb=" N GLN D 228 " --> pdb=" O GLN D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 246 Processing helix chain 'D' and resid 247 through 255 removed outlier: 3.771A pdb=" N ARG D 252 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 337 removed outlier: 3.519A pdb=" N GLN D 283 " --> pdb=" O VAL D 279 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU D 291 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU D 293 " --> pdb=" O LYS D 289 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU D 304 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 316 " --> pdb=" O THR D 312 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG D 335 " --> pdb=" O GLU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 391 removed outlier: 3.704A pdb=" N ALA D 344 " --> pdb=" O PRO D 340 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 389 " --> pdb=" O ARG D 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 26 Processing helix chain 'E' and resid 27 through 41 Processing helix chain 'F' and resid 7 through 32 Processing helix chain 'F' and resid 68 through 83 removed outlier: 4.423A pdb=" N ALA F 72 " --> pdb=" O LYS F 68 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS F 73 " --> pdb=" O SER F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 92 removed outlier: 3.624A pdb=" N GLU F 92 " --> pdb=" O GLU F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 111 through 127 removed outlier: 3.748A pdb=" N PHE F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA F 122 " --> pdb=" O ILE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 130 No H-bonds generated for 'chain 'F' and resid 128 through 130' Processing helix chain 'F' and resid 134 through 138 removed outlier: 3.889A pdb=" N ILE F 137 " --> pdb=" O ASN F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 156 Processing helix chain 'F' and resid 157 through 178 removed outlier: 3.520A pdb=" N ASP F 178 " --> pdb=" O LYS F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 257 removed outlier: 3.813A pdb=" N VAL F 244 " --> pdb=" O VAL F 240 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN F 246 " --> pdb=" O ARG F 242 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL F 247 " --> pdb=" O ASP F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 268 Processing helix chain 'h' and resid 4 through 10 removed outlier: 3.696A pdb=" N MET h 8 " --> pdb=" O ARG h 5 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS h 9 " --> pdb=" O PHE h 6 " (cutoff:3.500A) Processing helix chain 'h' and resid 75 through 80 Processing helix chain 'i' and resid 12 through 17 removed outlier: 3.583A pdb=" N GLN i 17 " --> pdb=" O PRO i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 19 through 27 removed outlier: 3.709A pdb=" N PHE i 24 " --> pdb=" O GLU i 20 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASN i 25 " --> pdb=" O GLU i 21 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR i 26 " --> pdb=" O GLU i 22 " (cutoff:3.500A) Processing helix chain 'i' and resid 29 through 38 Processing helix chain 'i' and resid 103 through 106 Processing helix chain 'j' and resid 4 through 13 Processing helix chain 'j' and resid 74 through 80 removed outlier: 3.774A pdb=" N LYS j 78 " --> pdb=" O ASP j 75 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 11 Processing helix chain 'l' and resid 16 through 28 removed outlier: 3.595A pdb=" N LEU l 20 " --> pdb=" O GLN l 16 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE l 21 " --> pdb=" O PRO l 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 6 through 15 Processing helix chain 'n' and resid 23 through 25 No H-bonds generated for 'chain 'n' and resid 23 through 25' Processing helix chain 'n' and resid 63 through 65 No H-bonds generated for 'chain 'n' and resid 63 through 65' Processing sheet with id=AA1, first strand: chain 'B' and resid 52 through 58 removed outlier: 4.164A pdb=" N ASP B 121 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N CYS B 46 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHE B 125 " --> pdb=" O CYS B 46 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 98 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 84 removed outlier: 5.249A pdb=" N ILE C 77 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLU C 98 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ARG C 79 " --> pdb=" O PHE C 96 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE C 96 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ARG C 81 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N TYR C 94 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL C 83 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AA4, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.830A pdb=" N TYR E 5 " --> pdb=" O PHE E 14 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE E 14 " --> pdb=" O TYR E 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 55 through 56 Processing sheet with id=AA6, first strand: chain 'F' and resid 107 through 109 Processing sheet with id=AA7, first strand: chain 'i' and resid 90 through 92 removed outlier: 3.525A pdb=" N TRP i 74 " --> pdb=" O LYS i 92 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N MET i 65 " --> pdb=" O PHE i 59 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE i 59 " --> pdb=" O MET i 65 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU i 67 " --> pdb=" O LYS i 57 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LYS i 57 " --> pdb=" O LEU i 67 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASN i 69 " --> pdb=" O ARG i 55 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG i 55 " --> pdb=" O ASN i 69 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU m 61 " --> pdb=" O ARG i 111 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N SER m 56 " --> pdb=" O ILE m 51 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE m 51 " --> pdb=" O SER m 56 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N HIS m 58 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLU m 49 " --> pdb=" O HIS m 58 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL m 62 " --> pdb=" O ALA m 45 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ALA m 45 " --> pdb=" O VAL m 62 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE m 64 " --> pdb=" O GLN m 43 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLN m 43 " --> pdb=" O ILE m 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'j' and resid 27 through 28 removed outlier: 6.466A pdb=" N THR j 19 " --> pdb=" O LEU j 71 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU j 71 " --> pdb=" O THR j 19 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLU j 21 " --> pdb=" O ARG j 69 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LYS k 64 " --> pdb=" O ARG k 49 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ARG k 49 " --> pdb=" O LYS k 64 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL k 66 " --> pdb=" O GLU k 47 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU k 47 " --> pdb=" O VAL k 66 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL k 70 " --> pdb=" O CYS k 43 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N CYS k 43 " --> pdb=" O VAL k 70 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU k 72 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ILE k 41 " --> pdb=" O LEU k 72 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU k 42 " --> pdb=" O LYS k 32 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LYS k 32 " --> pdb=" O LEU k 42 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ASP k 44 " --> pdb=" O THR k 30 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR k 30 " --> pdb=" O ASP k 44 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER k 79 " --> pdb=" O ILE k 20 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL k 82 " --> pdb=" O THR h 57 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR h 57 " --> pdb=" O VAL k 82 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR h 57 " --> pdb=" O LYS h 41 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS h 41 " --> pdb=" O THR h 57 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N SER h 59 " --> pdb=" O HIS h 39 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N HIS h 39 " --> pdb=" O SER h 59 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU h 40 " --> pdb=" O THR h 30 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N THR h 30 " --> pdb=" O LEU h 40 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ALA h 42 " --> pdb=" O THR h 28 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR h 28 " --> pdb=" O ALA h 42 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N THR h 14 " --> pdb=" O LEU h 70 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU h 70 " --> pdb=" O THR h 14 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N THR h 16 " --> pdb=" O PHE h 68 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N PHE h 68 " --> pdb=" O THR h 16 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLU h 18 " --> pdb=" O ARG h 66 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS i 98 " --> pdb=" O LEU h 70 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR i 95 " --> pdb=" O LYS i 71 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LYS i 71 " --> pdb=" O TYR i 95 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N SER i 97 " --> pdb=" O ASN i 69 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N MET i 65 " --> pdb=" O PHE i 59 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE i 59 " --> pdb=" O MET i 65 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU i 67 " --> pdb=" O LYS i 57 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LYS i 57 " --> pdb=" O LEU i 67 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASN i 69 " --> pdb=" O ARG i 55 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG i 55 " --> pdb=" O ASN i 69 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU m 61 " --> pdb=" O ARG i 111 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N SER m 56 " --> pdb=" O ILE m 51 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE m 51 " --> pdb=" O SER m 56 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N HIS m 58 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLU m 49 " --> pdb=" O HIS m 58 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL m 62 " --> pdb=" O ALA m 45 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ALA m 45 " --> pdb=" O VAL m 62 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE m 64 " --> pdb=" O GLN m 43 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLN m 43 " --> pdb=" O ILE m 64 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N GLN m 43 " --> pdb=" O VAL m 34 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL m 34 " --> pdb=" O GLN m 43 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR m 47 " --> pdb=" O LYS m 30 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS m 30 " --> pdb=" O THR m 47 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR m 71 " --> pdb=" O LYS m 22 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'j' and resid 31 through 35 removed outlier: 3.726A pdb=" N ILE j 33 " --> pdb=" O GLN j 42 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLN j 42 " --> pdb=" O ILE j 33 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN j 60 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET n 69 " --> pdb=" O LYS n 20 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY n 29 " --> pdb=" O LEU n 17 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN n 28 " --> pdb=" O CYS n 45 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS n 45 " --> pdb=" O GLN n 28 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL n 41 " --> pdb=" O ARG n 32 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'j' and resid 48 through 49 Processing sheet with id=AB2, first strand: chain 'l' and resid 71 through 75 removed outlier: 6.031A pdb=" N ALA l 61 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE l 43 " --> pdb=" O VAL l 33 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 96 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 1 1.18 - 1.34: 4101 1.34 - 1.50: 4151 1.50 - 1.66: 5250 1.66 - 1.82: 108 Bond restraints: 13611 Sorted by residual: bond pdb=" CG PRO k 85 " pdb=" CD PRO k 85 " ideal model delta sigma weight residual 1.503 1.022 0.481 3.40e-02 8.65e+02 2.00e+02 bond pdb=" N PRO k 85 " pdb=" CD PRO k 85 " ideal model delta sigma weight residual 1.473 1.573 -0.100 1.40e-02 5.10e+03 5.14e+01 bond pdb=" N PRO k 85 " pdb=" CA PRO k 85 " ideal model delta sigma weight residual 1.465 1.372 0.093 2.03e-02 2.43e+03 2.08e+01 bond pdb=" CB PRO k 85 " pdb=" CG PRO k 85 " ideal model delta sigma weight residual 1.492 1.678 -0.186 5.00e-02 4.00e+02 1.38e+01 bond pdb=" N9 G A 21 " pdb=" C4 G A 21 " ideal model delta sigma weight residual 1.375 1.391 -0.016 8.00e-03 1.56e+04 3.93e+00 ... (remaining 13606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.64: 18798 4.64 - 9.27: 49 9.27 - 13.91: 3 13.91 - 18.55: 5 18.55 - 23.18: 1 Bond angle restraints: 18856 Sorted by residual: angle pdb=" N PRO k 85 " pdb=" CD PRO k 85 " pdb=" CG PRO k 85 " ideal model delta sigma weight residual 103.20 80.02 23.18 1.50e+00 4.44e-01 2.39e+02 angle pdb=" CA PRO k 85 " pdb=" N PRO k 85 " pdb=" CD PRO k 85 " ideal model delta sigma weight residual 112.00 95.53 16.47 1.40e+00 5.10e-01 1.38e+02 angle pdb=" CA PRO k 85 " pdb=" CB PRO k 85 " pdb=" CG PRO k 85 " ideal model delta sigma weight residual 104.50 86.65 17.85 1.90e+00 2.77e-01 8.83e+01 angle pdb=" N ILE n 68 " pdb=" CA ILE n 68 " pdb=" C ILE n 68 " ideal model delta sigma weight residual 113.71 107.84 5.87 9.50e-01 1.11e+00 3.82e+01 angle pdb=" CG ARG D 256 " pdb=" CD ARG D 256 " pdb=" NE ARG D 256 " ideal model delta sigma weight residual 112.00 123.61 -11.61 2.20e+00 2.07e-01 2.78e+01 ... (remaining 18851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 7981 35.52 - 71.04: 547 71.04 - 106.56: 44 106.56 - 142.08: 5 142.08 - 177.60: 4 Dihedral angle restraints: 8581 sinusoidal: 4739 harmonic: 3842 Sorted by residual: dihedral pdb=" O4' U A 97 " pdb=" C1' U A 97 " pdb=" N1 U A 97 " pdb=" C2 U A 97 " ideal model delta sinusoidal sigma weight residual 232.00 78.01 153.99 1 1.70e+01 3.46e-03 6.31e+01 dihedral pdb=" O4' U A 86 " pdb=" C1' U A 86 " pdb=" N1 U A 86 " pdb=" C2 U A 86 " ideal model delta sinusoidal sigma weight residual -160.00 -61.88 -98.12 1 1.50e+01 4.44e-03 4.87e+01 dihedral pdb=" CA ILE n 68 " pdb=" C ILE n 68 " pdb=" N MET n 69 " pdb=" CA MET n 69 " ideal model delta harmonic sigma weight residual -180.00 -153.35 -26.65 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 8578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1727 0.055 - 0.110: 320 0.110 - 0.165: 132 0.165 - 0.220: 2 0.220 - 0.276: 1 Chirality restraints: 2182 Sorted by residual: chirality pdb=" CA PRO k 85 " pdb=" N PRO k 85 " pdb=" C PRO k 85 " pdb=" CB PRO k 85 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' U A 100 " pdb=" C4' U A 100 " pdb=" O3' U A 100 " pdb=" C2' U A 100 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" CA MET k 17 " pdb=" N MET k 17 " pdb=" C MET k 17 " pdb=" CB MET k 17 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 2179 not shown) Planarity restraints: 2015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 78 " -0.033 2.00e-02 2.50e+03 1.68e-02 6.33e+00 pdb=" N1 C A 78 " 0.034 2.00e-02 2.50e+03 pdb=" C2 C A 78 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C A 78 " 0.008 2.00e-02 2.50e+03 pdb=" N3 C A 78 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C A 78 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C A 78 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C A 78 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C A 78 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO k 85 " -0.040 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO k 86 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO k 86 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO k 86 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU k 83 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C GLU k 83 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU k 83 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY k 84 " -0.012 2.00e-02 2.50e+03 ... (remaining 2012 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 396 2.67 - 3.22: 12914 3.22 - 3.78: 22382 3.78 - 4.34: 29829 4.34 - 4.90: 44926 Nonbonded interactions: 110447 Sorted by model distance: nonbonded pdb=" O4 U A 109 " pdb=" O6 G A 126 " model vdw 2.108 2.432 nonbonded pdb=" OG SER h 35 " pdb=" OD1 ASN h 37 " model vdw 2.175 3.040 nonbonded pdb=" OP1 C A 108 " pdb=" NH1 ARG D 175 " model vdw 2.177 3.120 nonbonded pdb=" O GLY m 13 " pdb=" NZ LYS m 17 " model vdw 2.177 3.120 nonbonded pdb=" OP2 A A 88 " pdb=" OH TYR m 39 " model vdw 2.182 3.040 ... (remaining 110442 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 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: 7.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.670 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.481 13611 Z= 0.231 Angle : 0.826 23.184 18856 Z= 0.521 Chirality : 0.049 0.276 2182 Planarity : 0.005 0.061 2015 Dihedral : 21.126 177.605 6089 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.10 % Favored : 93.75 % Rotamer: Outliers : 0.26 % Allowed : 29.92 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.24), residues: 1296 helix: 0.37 (0.24), residues: 477 sheet: -1.31 (0.36), residues: 189 loop : -1.07 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D 256 TYR 0.030 0.002 TYR F 237 PHE 0.034 0.002 PHE h 6 TRP 0.010 0.001 TRP l 34 HIS 0.006 0.001 HIS l 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.23 (13611) covalent geometry : angle 0.82645 / 0.52 (18856) hydrogen bonds : bond 0.23941 / 24.65 ( 590) hydrogen bonds : angle 8.48687 / 11.33 ( 1603) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 174 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.0278 (mtt) cc_final: -0.0176 (mmp) REVERT: B 85 GLN cc_start: 0.7730 (pm20) cc_final: 0.7442 (pm20) REVERT: C 40 VAL cc_start: 0.8587 (p) cc_final: 0.8362 (m) REVERT: F 80 LEU cc_start: 0.8855 (mm) cc_final: 0.7893 (tp) REVERT: k 17 MET cc_start: 0.5782 (mmm) cc_final: 0.5069 (mmm) REVERT: k 83 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7348 (tm-30) REVERT: l 78 MET cc_start: 0.8570 (tmm) cc_final: 0.8249 (tmm) outliers start: 3 outliers final: 1 residues processed: 176 average time/residue: 0.1040 time to fit residues: 26.5834 Evaluate side-chains 164 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 311 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN ** F 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 39 ASN j 40 ASN ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 40 ASN l 65 HIS ** n 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.115646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.091130 restraints weight = 59371.978| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 4.66 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 13611 Z= 0.153 Angle : 0.676 10.396 18856 Z= 0.361 Chirality : 0.043 0.363 2182 Planarity : 0.005 0.056 2015 Dihedral : 20.218 174.242 3271 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.98 % Rotamer: Outliers : 3.50 % Allowed : 24.13 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.23), residues: 1296 helix: 0.52 (0.23), residues: 479 sheet: -1.47 (0.35), residues: 191 loop : -1.06 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 130 TYR 0.019 0.002 TYR F 237 PHE 0.031 0.002 PHE F 98 TRP 0.009 0.001 TRP l 34 HIS 0.007 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (13611) covalent geometry : angle 0.67609 / 0.36 (18856) hydrogen bonds : bond 0.06253 / 6.58 ( 590) hydrogen bonds : angle 6.13055 / 8.04 ( 1603) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 ASP cc_start: 0.8197 (t0) cc_final: 0.7961 (t70) REVERT: B 76 LEU cc_start: 0.8591 (mt) cc_final: 0.8325 (pp) REVERT: C 40 VAL cc_start: 0.8441 (p) cc_final: 0.8234 (m) REVERT: D 255 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7365 (tp30) REVERT: F 75 MET cc_start: 0.5318 (mmp) cc_final: 0.4784 (mmp) REVERT: F 242 ARG cc_start: 0.8756 (tpm170) cc_final: 0.8467 (tpm170) REVERT: h 55 LEU cc_start: 0.8649 (tp) cc_final: 0.8180 (tp) REVERT: k 17 MET cc_start: 0.6512 (mmm) cc_final: 0.6255 (mmm) REVERT: l 78 MET cc_start: 0.7512 (tmm) cc_final: 0.7161 (tmm) outliers start: 41 outliers final: 20 residues processed: 213 average time/residue: 0.1053 time to fit residues: 32.8048 Evaluate side-chains 187 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain j residue 37 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain l residue 70 SER Chi-restraints excluded: chain l residue 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 0.8980 chunk 69 optimal weight: 0.0980 chunk 111 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 131 optimal weight: 0.0270 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN E 24 HIS E 30 HIS ** F 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 39 ASN ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.115758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.091384 restraints weight = 59893.627| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 4.62 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13611 Z= 0.135 Angle : 0.633 10.934 18856 Z= 0.337 Chirality : 0.042 0.355 2182 Planarity : 0.004 0.049 2015 Dihedral : 20.091 172.638 3269 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.33 % Favored : 93.52 % Rotamer: Outliers : 3.41 % Allowed : 25.06 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.23), residues: 1296 helix: 0.56 (0.23), residues: 481 sheet: -1.38 (0.37), residues: 174 loop : -1.17 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 196 TYR 0.012 0.001 TYR F 237 PHE 0.036 0.002 PHE F 98 TRP 0.007 0.001 TRP E 37 HIS 0.010 0.001 HIS n 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (13611) covalent geometry : angle 0.63328 / 0.34 (18856) hydrogen bonds : bond 0.05613 / 5.86 ( 590) hydrogen bonds : angle 5.76958 / 7.63 ( 1603) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8380 (mt) REVERT: B 65 ASP cc_start: 0.8240 (t0) cc_final: 0.7949 (t70) REVERT: B 76 LEU cc_start: 0.8677 (mt) cc_final: 0.8464 (pp) REVERT: D 255 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7231 (tp30) REVERT: F 75 MET cc_start: 0.5057 (mmp) cc_final: 0.4535 (mmp) REVERT: F 117 GLN cc_start: 0.7913 (tt0) cc_final: 0.7650 (tm-30) REVERT: F 242 ARG cc_start: 0.8711 (tpm170) cc_final: 0.8225 (tpm170) REVERT: h 55 LEU cc_start: 0.8603 (tp) cc_final: 0.8123 (tp) REVERT: k 17 MET cc_start: 0.6680 (mmm) cc_final: 0.6290 (mmm) REVERT: l 78 MET cc_start: 0.7649 (tmm) cc_final: 0.7231 (tmm) outliers start: 40 outliers final: 18 residues processed: 211 average time/residue: 0.1185 time to fit residues: 36.2737 Evaluate side-chains 190 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 74 LEU Chi-restraints excluded: chain j residue 37 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain l residue 70 SER Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain n residue 9 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 116 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 95 optimal weight: 0.0050 chunk 37 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 135 optimal weight: 0.4980 chunk 69 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN i 39 ASN ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 40 ASN ** n 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.114784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.090366 restraints weight = 59949.955| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 4.58 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13611 Z= 0.150 Angle : 0.628 10.589 18856 Z= 0.335 Chirality : 0.042 0.354 2182 Planarity : 0.005 0.071 2015 Dihedral : 20.062 172.373 3269 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.40 % Favored : 93.44 % Rotamer: Outliers : 3.24 % Allowed : 26.68 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.23), residues: 1296 helix: 0.59 (0.23), residues: 483 sheet: -1.64 (0.36), residues: 179 loop : -1.19 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG k 16 TYR 0.037 0.002 TYR F 237 PHE 0.026 0.002 PHE h 6 TRP 0.006 0.001 TRP C 32 HIS 0.004 0.001 HIS l 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (13611) covalent geometry : angle 0.62815 / 0.33 (18856) hydrogen bonds : bond 0.05317 / 5.49 ( 590) hydrogen bonds : angle 5.66855 / 7.45 ( 1603) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8313 (mt) REVERT: B 65 ASP cc_start: 0.8302 (t0) cc_final: 0.8030 (m-30) REVERT: B 76 LEU cc_start: 0.8727 (mt) cc_final: 0.8513 (pp) REVERT: D 255 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7223 (tp30) REVERT: F 75 MET cc_start: 0.5080 (mmp) cc_final: 0.4616 (mmp) REVERT: F 117 GLN cc_start: 0.7948 (tt0) cc_final: 0.7677 (tm-30) REVERT: F 242 ARG cc_start: 0.8750 (tpm170) cc_final: 0.8358 (tpm170) REVERT: h 55 LEU cc_start: 0.8608 (tp) cc_final: 0.8220 (tp) REVERT: k 17 MET cc_start: 0.6534 (mmm) cc_final: 0.5756 (mmm) REVERT: k 27 PHE cc_start: 0.8218 (t80) cc_final: 0.7907 (t80) REVERT: k 80 MET cc_start: 0.8015 (tmm) cc_final: 0.7611 (tmm) REVERT: l 78 MET cc_start: 0.7656 (tmm) cc_final: 0.7228 (tmm) REVERT: m 20 MET cc_start: 0.6541 (OUTLIER) cc_final: 0.6137 (mmt) REVERT: m 49 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.5402 (tt0) REVERT: n 70 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6565 (pp) outliers start: 38 outliers final: 19 residues processed: 213 average time/residue: 0.1223 time to fit residues: 37.4998 Evaluate side-chains 188 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain j residue 37 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain m residue 20 MET Chi-restraints excluded: chain m residue 49 GLU Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 48 MET Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 70 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 2 optimal weight: 20.0000 chunk 89 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 81 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 39 ASN ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.114663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.090353 restraints weight = 60128.908| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 4.62 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13611 Z= 0.148 Angle : 0.637 10.628 18856 Z= 0.338 Chirality : 0.042 0.352 2182 Planarity : 0.004 0.057 2015 Dihedral : 20.058 172.178 3269 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.64 % Favored : 93.21 % Rotamer: Outliers : 3.58 % Allowed : 26.34 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.23), residues: 1296 helix: 0.59 (0.23), residues: 482 sheet: -1.58 (0.37), residues: 179 loop : -1.20 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 196 TYR 0.043 0.002 TYR F 237 PHE 0.028 0.002 PHE h 6 TRP 0.007 0.001 TRP C 32 HIS 0.008 0.001 HIS n 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (13611) covalent geometry : angle 0.63652 / 0.34 (18856) hydrogen bonds : bond 0.05169 / 5.34 ( 590) hydrogen bonds : angle 5.54379 / 7.27 ( 1603) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8544 (mm) REVERT: B 65 ASP cc_start: 0.8302 (t0) cc_final: 0.8077 (m-30) REVERT: D 255 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7248 (tp30) REVERT: F 75 MET cc_start: 0.4999 (mmp) cc_final: 0.4453 (mmp) REVERT: F 117 GLN cc_start: 0.7949 (tt0) cc_final: 0.7670 (tm-30) REVERT: F 242 ARG cc_start: 0.8725 (tpm170) cc_final: 0.8345 (tpm170) REVERT: h 45 MET cc_start: 0.8076 (tmm) cc_final: 0.7690 (tmm) REVERT: h 55 LEU cc_start: 0.8597 (tp) cc_final: 0.8328 (tp) REVERT: k 17 MET cc_start: 0.6432 (mmm) cc_final: 0.5783 (mmm) REVERT: k 80 MET cc_start: 0.8076 (tmm) cc_final: 0.7661 (tmm) REVERT: l 78 MET cc_start: 0.7698 (tmm) cc_final: 0.7258 (tmm) REVERT: m 20 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.6102 (mmt) REVERT: m 49 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.5578 (tt0) outliers start: 42 outliers final: 26 residues processed: 209 average time/residue: 0.1048 time to fit residues: 31.8211 Evaluate side-chains 196 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 67 LEU Chi-restraints excluded: chain j residue 37 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 79 ASN Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain l residue 54 MET Chi-restraints excluded: chain l residue 58 LEU Chi-restraints excluded: chain l residue 84 ILE Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain m residue 19 VAL Chi-restraints excluded: chain m residue 20 MET Chi-restraints excluded: chain m residue 49 GLU Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 60 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 22 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN F 255 HIS F 260 GLN ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 ASN ** 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 = 0.4438 r_free = 0.4438 target = 0.113540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.089190 restraints weight = 59704.566| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 4.50 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13611 Z= 0.171 Angle : 0.655 10.407 18856 Z= 0.347 Chirality : 0.042 0.349 2182 Planarity : 0.004 0.063 2015 Dihedral : 20.074 172.078 3269 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.87 % Favored : 92.98 % Rotamer: Outliers : 3.67 % Allowed : 26.94 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.23), residues: 1296 helix: 0.58 (0.23), residues: 483 sheet: -1.61 (0.37), residues: 179 loop : -1.19 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 306 TYR 0.017 0.002 TYR m 71 PHE 0.027 0.002 PHE h 6 TRP 0.006 0.001 TRP C 32 HIS 0.013 0.001 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (13611) covalent geometry : angle 0.65550 / 0.35 (18856) hydrogen bonds : bond 0.05263 / 5.46 ( 590) hydrogen bonds : angle 5.54922 / 7.26 ( 1603) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8526 (mm) REVERT: B 65 ASP cc_start: 0.8320 (t0) cc_final: 0.8104 (m-30) REVERT: B 76 LEU cc_start: 0.8522 (pp) cc_final: 0.8244 (mt) REVERT: D 255 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7275 (tp30) REVERT: D 353 GLN cc_start: 0.9177 (mt0) cc_final: 0.8941 (mt0) REVERT: F 75 MET cc_start: 0.5041 (mmp) cc_final: 0.4435 (mmp) REVERT: F 117 GLN cc_start: 0.7982 (tt0) cc_final: 0.7695 (tm-30) REVERT: F 242 ARG cc_start: 0.8782 (tpm170) cc_final: 0.8359 (tpm170) REVERT: h 55 LEU cc_start: 0.8624 (tp) cc_final: 0.8357 (tp) REVERT: k 17 MET cc_start: 0.6401 (mmm) cc_final: 0.5945 (mmm) REVERT: k 27 PHE cc_start: 0.8146 (t80) cc_final: 0.7854 (t80) REVERT: k 80 MET cc_start: 0.8088 (tmm) cc_final: 0.7706 (tmm) REVERT: l 78 MET cc_start: 0.7703 (tmm) cc_final: 0.7250 (tmm) REVERT: m 49 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5778 (tt0) outliers start: 43 outliers final: 28 residues processed: 203 average time/residue: 0.0963 time to fit residues: 28.9410 Evaluate side-chains 195 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 260 GLN Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain i residue 67 LEU Chi-restraints excluded: chain j residue 37 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 79 ASN Chi-restraints excluded: chain k residue 19 CYS Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain l residue 54 MET Chi-restraints excluded: chain l residue 84 ILE Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain m residue 19 VAL Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain m residue 49 GLU Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 48 MET Chi-restraints excluded: chain n residue 60 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 110 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 86 optimal weight: 0.0670 chunk 63 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 125 optimal weight: 0.0270 chunk 96 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 HIS E 20 ASN F 255 HIS ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 76 ASN ** l 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.114038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.093081 restraints weight = 59559.342| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 4.69 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13611 Z= 0.136 Angle : 0.649 11.574 18856 Z= 0.338 Chirality : 0.042 0.350 2182 Planarity : 0.004 0.061 2015 Dihedral : 20.060 171.954 3269 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.56 % Favored : 93.29 % Rotamer: Outliers : 3.32 % Allowed : 27.11 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.23), residues: 1296 helix: 0.69 (0.23), residues: 482 sheet: -1.50 (0.37), residues: 183 loop : -1.14 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 306 TYR 0.018 0.001 TYR F 237 PHE 0.031 0.002 PHE h 6 TRP 0.008 0.001 TRP F 256 HIS 0.011 0.001 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (13611) covalent geometry : angle 0.64934 / 0.34 (18856) hydrogen bonds : bond 0.04877 / 5.05 ( 590) hydrogen bonds : angle 5.40354 / 7.09 ( 1603) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8537 (mm) REVERT: B 76 LEU cc_start: 0.8603 (pp) cc_final: 0.8314 (mt) REVERT: D 255 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7327 (tp30) REVERT: F 75 MET cc_start: 0.5081 (mmp) cc_final: 0.4549 (mmp) REVERT: F 117 GLN cc_start: 0.7947 (tt0) cc_final: 0.7684 (tm-30) REVERT: F 242 ARG cc_start: 0.8768 (tpm170) cc_final: 0.8380 (tpm170) REVERT: h 55 LEU cc_start: 0.8619 (tp) cc_final: 0.8347 (tp) REVERT: k 16 ARG cc_start: 0.7077 (mpt180) cc_final: 0.6836 (mmt180) REVERT: k 17 MET cc_start: 0.6196 (mmm) cc_final: 0.5695 (mmm) REVERT: k 27 PHE cc_start: 0.8323 (t80) cc_final: 0.8069 (t80) REVERT: k 80 MET cc_start: 0.8060 (tmm) cc_final: 0.7748 (tmm) REVERT: l 78 MET cc_start: 0.7270 (tmm) cc_final: 0.6570 (tmm) REVERT: m 49 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5549 (tt0) outliers start: 39 outliers final: 26 residues processed: 211 average time/residue: 0.1051 time to fit residues: 31.8739 Evaluate side-chains 199 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain i residue 67 LEU Chi-restraints excluded: chain j residue 37 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 19 CYS Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain l residue 84 ILE Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain m residue 19 VAL Chi-restraints excluded: chain m residue 49 GLU Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 48 MET Chi-restraints excluded: chain n residue 60 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 10 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 3 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS h 39 HIS ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 16 GLN l 40 ASN ** l 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.108548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.088281 restraints weight = 59872.804| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 4.42 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 13611 Z= 0.325 Angle : 0.834 9.761 18856 Z= 0.442 Chirality : 0.051 0.340 2182 Planarity : 0.007 0.085 2015 Dihedral : 20.354 172.302 3269 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.26 % Favored : 91.51 % Rotamer: Outliers : 4.18 % Allowed : 28.05 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.23), residues: 1296 helix: -0.00 (0.23), residues: 483 sheet: -1.77 (0.36), residues: 196 loop : -1.35 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 356 TYR 0.034 0.003 TYR l 36 PHE 0.027 0.003 PHE h 6 TRP 0.016 0.002 TRP B 89 HIS 0.014 0.002 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.33 (13611) covalent geometry : angle 0.83437 / 0.44 (18856) hydrogen bonds : bond 0.07215 / 7.58 ( 590) hydrogen bonds : angle 6.00671 / 7.80 ( 1603) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 159 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8295 (mm) REVERT: B 48 MET cc_start: 0.7675 (mmp) cc_final: 0.7418 (mmt) REVERT: B 76 LEU cc_start: 0.8698 (pp) cc_final: 0.8380 (mt) REVERT: D 255 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7372 (tp30) REVERT: D 356 ARG cc_start: 0.7449 (mtt-85) cc_final: 0.7112 (tpt-90) REVERT: F 75 MET cc_start: 0.5070 (mmp) cc_final: 0.4489 (mmt) REVERT: F 242 ARG cc_start: 0.8841 (tpm170) cc_final: 0.8400 (tpm170) REVERT: h 74 LEU cc_start: 0.3838 (OUTLIER) cc_final: 0.3626 (mm) REVERT: k 16 ARG cc_start: 0.7388 (mpt180) cc_final: 0.6854 (mmt180) REVERT: k 17 MET cc_start: 0.6392 (mmm) cc_final: 0.5831 (mmm) REVERT: k 27 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.8034 (t80) REVERT: k 80 MET cc_start: 0.8133 (tmm) cc_final: 0.7823 (tmm) REVERT: l 78 MET cc_start: 0.7783 (tmm) cc_final: 0.7373 (tmm) REVERT: m 20 MET cc_start: 0.5795 (OUTLIER) cc_final: 0.5152 (mmt) REVERT: m 40 MET cc_start: 0.7117 (mpp) cc_final: 0.6723 (mtt) REVERT: m 49 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5975 (tt0) outliers start: 49 outliers final: 33 residues processed: 194 average time/residue: 0.1126 time to fit residues: 31.6200 Evaluate side-chains 187 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 74 LEU Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain i residue 67 LEU Chi-restraints excluded: chain j residue 37 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 19 CYS Chi-restraints excluded: chain k residue 27 PHE Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain l residue 40 ASN Chi-restraints excluded: chain l residue 58 LEU Chi-restraints excluded: chain l residue 84 ILE Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain m residue 20 MET Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain m residue 49 GLU Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 19 LEU Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain n residue 60 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 78 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 40 ASN ** l 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 67 ASN ** 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 = 0.4411 r_free = 0.4411 target = 0.111509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.087020 restraints weight = 60288.952| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 4.53 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13611 Z= 0.158 Angle : 0.715 11.842 18856 Z= 0.374 Chirality : 0.044 0.344 2182 Planarity : 0.005 0.064 2015 Dihedral : 20.351 172.766 3269 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.71 % Favored : 93.13 % Rotamer: Outliers : 2.98 % Allowed : 29.41 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.23), residues: 1296 helix: 0.36 (0.23), residues: 481 sheet: -1.54 (0.39), residues: 169 loop : -1.28 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG n 63 TYR 0.017 0.002 TYR F 237 PHE 0.038 0.003 PHE j 70 TRP 0.009 0.001 TRP C 32 HIS 0.017 0.002 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (13611) covalent geometry : angle 0.71503 / 0.37 (18856) hydrogen bonds : bond 0.05329 / 5.54 ( 590) hydrogen bonds : angle 5.61478 / 7.35 ( 1603) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8335 (mm) REVERT: B 48 MET cc_start: 0.7577 (mmp) cc_final: 0.7263 (mmt) REVERT: B 76 LEU cc_start: 0.8592 (pp) cc_final: 0.8288 (mt) REVERT: D 255 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7327 (tp30) REVERT: D 356 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7306 (tpt-90) REVERT: F 75 MET cc_start: 0.4977 (mmp) cc_final: 0.4721 (mmt) REVERT: F 242 ARG cc_start: 0.8915 (tpm170) cc_final: 0.8532 (tpm170) REVERT: h 55 LEU cc_start: 0.8590 (tp) cc_final: 0.8302 (tp) REVERT: h 74 LEU cc_start: 0.4138 (OUTLIER) cc_final: 0.3923 (mm) REVERT: k 17 MET cc_start: 0.6415 (mmm) cc_final: 0.6135 (mmm) REVERT: k 18 ARG cc_start: 0.7827 (tmm160) cc_final: 0.7608 (tmm160) REVERT: k 27 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7908 (t80) REVERT: l 78 MET cc_start: 0.7667 (tmm) cc_final: 0.7250 (tmm) REVERT: m 20 MET cc_start: 0.6322 (OUTLIER) cc_final: 0.5864 (mmt) REVERT: m 49 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.5886 (tt0) outliers start: 35 outliers final: 27 residues processed: 186 average time/residue: 0.1041 time to fit residues: 28.3929 Evaluate side-chains 190 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 74 LEU Chi-restraints excluded: chain i residue 67 LEU Chi-restraints excluded: chain j residue 37 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 72 ILE Chi-restraints excluded: chain k residue 19 CYS Chi-restraints excluded: chain k residue 27 PHE Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain l residue 40 ASN Chi-restraints excluded: chain l residue 84 ILE Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain m residue 19 VAL Chi-restraints excluded: chain m residue 20 MET Chi-restraints excluded: chain m residue 49 GLU Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 19 LEU Chi-restraints excluded: chain n residue 44 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 138 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 64 optimal weight: 50.0000 chunk 98 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS h 12 HIS ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 67 ASN ** 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 = 0.4417 r_free = 0.4417 target = 0.111899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.089863 restraints weight = 59960.782| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 5.19 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13611 Z= 0.151 Angle : 0.712 13.347 18856 Z= 0.369 Chirality : 0.044 0.344 2182 Planarity : 0.005 0.063 2015 Dihedral : 20.227 172.357 3269 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.02 % Favored : 92.82 % Rotamer: Outliers : 2.81 % Allowed : 30.01 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.23), residues: 1296 helix: 0.48 (0.23), residues: 482 sheet: -1.39 (0.39), residues: 169 loop : -1.25 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 306 TYR 0.020 0.002 TYR F 237 PHE 0.037 0.002 PHE h 6 TRP 0.008 0.001 TRP F 256 HIS 0.015 0.002 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (13611) covalent geometry : angle 0.71242 / 0.37 (18856) hydrogen bonds : bond 0.05104 / 5.25 ( 590) hydrogen bonds : angle 5.50681 / 7.22 ( 1603) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8392 (mm) REVERT: B 48 MET cc_start: 0.7520 (mmp) cc_final: 0.7240 (mmt) REVERT: B 76 LEU cc_start: 0.8626 (pp) cc_final: 0.8330 (mt) REVERT: D 255 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7394 (tp30) REVERT: D 356 ARG cc_start: 0.7690 (mtt-85) cc_final: 0.7244 (tpt-90) REVERT: F 75 MET cc_start: 0.5200 (mmp) cc_final: 0.4985 (mmt) REVERT: F 242 ARG cc_start: 0.8912 (tpm170) cc_final: 0.8471 (tpm170) REVERT: h 55 LEU cc_start: 0.8604 (tp) cc_final: 0.8311 (tp) REVERT: h 74 LEU cc_start: 0.3885 (OUTLIER) cc_final: 0.3669 (mm) REVERT: k 27 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8140 (t80) REVERT: l 78 MET cc_start: 0.7595 (tmm) cc_final: 0.7064 (tmm) REVERT: m 20 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.6098 (mmt) REVERT: m 49 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.5748 (tt0) REVERT: n 13 MET cc_start: 0.6976 (tpp) cc_final: 0.6352 (tpp) outliers start: 33 outliers final: 23 residues processed: 187 average time/residue: 0.1135 time to fit residues: 30.9355 Evaluate side-chains 188 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain h residue 74 LEU Chi-restraints excluded: chain i residue 67 LEU Chi-restraints excluded: chain j residue 37 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 79 ASN Chi-restraints excluded: chain k residue 19 CYS Chi-restraints excluded: chain k residue 27 PHE Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain l residue 84 ILE Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain m residue 19 VAL Chi-restraints excluded: chain m residue 20 MET Chi-restraints excluded: chain m residue 49 GLU Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 0.0670 chunk 21 optimal weight: 0.0870 chunk 113 optimal weight: 2.9990 chunk 77 optimal weight: 0.0770 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.112688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.091121 restraints weight = 58974.666| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 4.76 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13611 Z= 0.143 Angle : 0.720 13.063 18856 Z= 0.372 Chirality : 0.044 0.346 2182 Planarity : 0.005 0.074 2015 Dihedral : 20.114 172.093 3269 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.40 % Favored : 93.44 % Rotamer: Outliers : 2.39 % Allowed : 30.69 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.24), residues: 1296 helix: 0.48 (0.23), residues: 483 sheet: -1.40 (0.39), residues: 181 loop : -1.18 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG k 16 TYR 0.018 0.001 TYR F 237 PHE 0.038 0.002 PHE h 6 TRP 0.010 0.001 TRP F 256 HIS 0.023 0.002 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (13611) covalent geometry : angle 0.71961 / 0.37 (18856) hydrogen bonds : bond 0.04876 / 5.02 ( 590) hydrogen bonds : angle 5.46786 / 7.27 ( 1603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3235.81 seconds wall clock time: 56 minutes 15.54 seconds (3375.54 seconds total)