Starting phenix.real_space_refine on Fri Jul 3 08:03:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r7n_18984/07_2026/8r7n_18984.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r7n_18984/07_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_18984/07_2026/8r7n_18984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r7n_18984/07_2026/8r7n_18984.map" model { file = "/net/cci-nas-00/data/ceres_data/8r7n_18984/07_2026/8r7n_18984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r7n_18984/07_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-dev-6108/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: 2.95, per 1000 atoms: 0.22 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: 1.07 Conformation dependent library (CDL) restraints added in 515.1 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: 1.71 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: 2.28 Time building geometry restraints manager: 1.45 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: 1842 0.055 - 0.110: 294 0.110 - 0.165: 43 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: 5.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.890 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.370 ------------------------------------------------------------------------------- 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= 0.224 Angle : 0.769 23.184 18856 Z= 0.459 Chirality : 0.040 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 0.00562 / 0.22 (13611) covalent geometry : angle 0.76927 / 0.46 (18856) hydrogen bonds : bond 0.23941 / 22.58 ( 590) hydrogen bonds : angle 8.48687 / 10.96 ( 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 : 0.429 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: 0.1186 time to fit residues: 30.2642 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 : 0.375 ------------------------------------------------------------------------------- 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: 9.9990 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 = 0.4458 r_free = 0.4458 target = 0.115637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.091270 restraints weight = 59420.035| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 4.58 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 13611 Z= 0.152 Angle : 0.665 10.476 18856 Z= 0.358 Chirality : 0.042 0.236 2182 Planarity : 0.005 0.059 2015 Dihedral : 20.318 172.593 3271 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.98 % Rotamer: Outliers : 3.41 % Allowed : 24.13 % Favored : 72.46 % 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: 0.50 (0.23), residues: 481 sheet: -1.46 (0.35), residues: 191 loop : -1.07 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 245 TYR 0.018 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 l 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (13611) covalent geometry : angle 0.66527 / 0.36 (18856) hydrogen bonds : bond 0.06270 / 6.02 ( 590) hydrogen bonds : angle 6.13381 / 7.80 ( 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 225 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.588 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: 0.8215 (t0) cc_final: 0.7978 (t70) REVERT: B 76 LEU cc_start: 0.8603 (mt) cc_final: 0.8319 (pp) REVERT: C 40 VAL cc_start: 0.8474 (p) cc_final: 0.8261 (m) REVERT: D 255 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7357 (tp30) REVERT: F 75 MET cc_start: 0.5187 (mmp) cc_final: 0.4656 (mmp) REVERT: F 242 ARG cc_start: 0.8772 (tpm170) cc_final: 0.8480 (tpm170) REVERT: h 55 LEU cc_start: 0.8647 (tp) cc_final: 0.8179 (tp) REVERT: k 17 MET cc_start: 0.6544 (mmm) cc_final: 0.6293 (mmm) REVERT: l 78 MET cc_start: 0.7520 (tmm) cc_final: 0.7204 (tmm) REVERT: n 69 MET cc_start: 0.4081 (tpp) cc_final: 0.3177 (tpp) outliers start: 40 outliers final: 19 residues processed: 213 average time/residue: 0.1102 time to fit residues: 34.2319 Evaluate side-chains 185 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 123 VAL 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 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 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: 0.7980 chunk 69 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 131 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.115473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.090977 restraints weight = 60437.248| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 4.66 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.1340 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= 0.142 Angle : 0.632 10.975 18856 Z= 0.338 Chirality : 0.041 0.238 2182 Planarity : 0.004 0.050 2015 Dihedral : 20.250 171.547 3269 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.48 % Favored : 93.36 % Rotamer: Outliers : 3.84 % Allowed : 24.89 % Favored : 71.27 % 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: 0.50 (0.23), residues: 482 sheet: -1.44 (0.37), residues: 174 loop : -1.16 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 196 TYR 0.012 0.001 TYR m 71 PHE 0.035 0.002 PHE F 98 TRP 0.008 0.001 TRP l 34 HIS 0.012 0.001 HIS n 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (13611) covalent geometry : angle 0.63217 / 0.34 (18856) hydrogen bonds : bond 0.05707 / 5.43 ( 590) hydrogen bonds : angle 5.87437 / 7.56 ( 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 222 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 0.430 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: 0.8806 (OUTLIER) cc_final: 0.8401 (mt) REVERT: B 65 ASP cc_start: 0.8242 (t0) cc_final: 0.7957 (t70) REVERT: B 76 LEU cc_start: 0.8634 (mt) cc_final: 0.8428 (pp) REVERT: D 255 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7308 (tp30) REVERT: F 117 GLN cc_start: 0.7915 (tt0) cc_final: 0.7639 (tm-30) REVERT: F 242 ARG cc_start: 0.8771 (tpm170) cc_final: 0.8250 (tpm170) REVERT: h 55 LEU cc_start: 0.8632 (tp) cc_final: 0.8145 (tp) REVERT: k 17 MET cc_start: 0.6747 (mmm) cc_final: 0.6238 (mmm) REVERT: l 78 MET cc_start: 0.7603 (tmm) cc_final: 0.7191 (tmm) outliers start: 45 outliers final: 23 residues processed: 209 average time/residue: 0.1110 time to fit residues: 33.6892 Evaluate side-chains 191 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 123 VAL 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 311 ASP 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 32 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 19 CYS Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 34 PHE 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: 10.0000 chunk 115 optimal weight: 10.0000 chunk 95 optimal weight: 0.0020 chunk 37 optimal weight: 9.9990 chunk 76 optimal weight: 0.1980 chunk 135 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 overall best weight: 1.9792 ------------------------------------------------------------------------------- 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 24 HIS h 39 HIS 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 5 HIS ** n 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.113098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.088571 restraints weight = 60194.399| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 4.51 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13611 Z= 0.184 Angle : 0.645 10.203 18856 Z= 0.349 Chirality : 0.042 0.253 2182 Planarity : 0.005 0.069 2015 Dihedral : 20.271 171.223 3269 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.56 % Favored : 93.29 % Rotamer: Outliers : 3.50 % Allowed : 26.68 % 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: -1.02 (0.23), residues: 1296 helix: 0.47 (0.23), residues: 483 sheet: -1.79 (0.36), residues: 180 loop : -1.19 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG k 18 TYR 0.041 0.002 TYR F 237 PHE 0.027 0.002 PHE F 98 TRP 0.006 0.001 TRP C 32 HIS 0.007 0.001 HIS n 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (13611) covalent geometry : angle 0.64492 / 0.35 (18856) hydrogen bonds : bond 0.05704 / 5.46 ( 590) hydrogen bonds : angle 5.79315 / 7.34 ( 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 215 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.485 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: B 35 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8275 (mt) REVERT: B 65 ASP cc_start: 0.8288 (t0) cc_final: 0.8049 (m-30) REVERT: D 255 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7255 (tp30) REVERT: F 117 GLN cc_start: 0.7975 (tt0) cc_final: 0.7701 (tm-30) REVERT: F 242 ARG cc_start: 0.8765 (tpm170) cc_final: 0.8327 (tpm170) REVERT: h 55 LEU cc_start: 0.8670 (tp) cc_final: 0.8294 (tp) REVERT: k 17 MET cc_start: 0.6351 (mmm) cc_final: 0.5935 (mmm) REVERT: k 27 PHE cc_start: 0.8184 (t80) cc_final: 0.7949 (t80) REVERT: k 80 MET cc_start: 0.8149 (tmm) cc_final: 0.7545 (tmm) REVERT: l 78 MET cc_start: 0.7669 (tmm) cc_final: 0.7298 (tmm) REVERT: m 49 GLU cc_start: 0.6335 (OUTLIER) cc_final: 0.5703 (tt0) outliers start: 41 outliers final: 25 residues processed: 206 average time/residue: 0.1173 time to fit residues: 34.9532 Evaluate side-chains 184 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 123 VAL Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain D residue 197 GLU 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 2 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 39 ASN ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 76 ASN ** l 40 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 = 0.4435 r_free = 0.4435 target = 0.113315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.091412 restraints weight = 60265.359| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 4.61 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2006 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= 0.161 Angle : 0.654 10.707 18856 Z= 0.347 Chirality : 0.043 0.260 2182 Planarity : 0.005 0.058 2015 Dihedral : 20.304 171.255 3269 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.40 % Favored : 93.44 % Rotamer: Outliers : 4.26 % Allowed : 27.11 % Favored : 68.63 % 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: -1.01 (0.23), residues: 1296 helix: 0.49 (0.23), residues: 483 sheet: -1.78 (0.37), residues: 180 loop : -1.19 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 196 TYR 0.042 0.002 TYR F 237 PHE 0.042 0.002 PHE F 98 TRP 0.007 0.001 TRP C 32 HIS 0.008 0.001 HIS E 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (13611) covalent geometry : angle 0.65413 / 0.35 (18856) hydrogen bonds : bond 0.05289 / 5.02 ( 590) hydrogen bonds : angle 5.62844 / 7.16 ( 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 226 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 176 time to evaluate : 0.443 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: 0.8781 (OUTLIER) cc_final: 0.8570 (mm) REVERT: B 65 ASP cc_start: 0.8287 (t0) cc_final: 0.8068 (m-30) REVERT: B 76 LEU cc_start: 0.8523 (pp) cc_final: 0.8264 (mt) REVERT: D 255 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7332 (tp30) REVERT: E 38 TYR cc_start: 0.6995 (m-80) cc_final: 0.6760 (m-80) REVERT: F 117 GLN cc_start: 0.7964 (tt0) cc_final: 0.7706 (tm-30) REVERT: F 242 ARG cc_start: 0.8725 (tpm170) cc_final: 0.8332 (tpm170) REVERT: h 55 LEU cc_start: 0.8669 (tp) cc_final: 0.8397 (tp) REVERT: k 17 MET cc_start: 0.6115 (mmm) cc_final: 0.5401 (mmm) REVERT: k 80 MET cc_start: 0.7964 (tmm) cc_final: 0.7734 (tmm) REVERT: l 78 MET cc_start: 0.7582 (tmm) cc_final: 0.7111 (tmm) REVERT: m 20 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.5917 (mmt) REVERT: m 49 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5595 (tt0) outliers start: 50 outliers final: 29 residues processed: 214 average time/residue: 0.1085 time to fit residues: 33.7011 Evaluate side-chains 191 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 123 VAL Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain D residue 197 GLU 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 311 ASP Chi-restraints excluded: chain D residue 364 GLU 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 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 48 MET 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: 3.9990 chunk 127 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** F 260 GLN ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.113011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.088586 restraints weight = 59549.859| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 4.50 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13611 Z= 0.162 Angle : 0.652 10.557 18856 Z= 0.345 Chirality : 0.043 0.254 2182 Planarity : 0.004 0.062 2015 Dihedral : 20.300 171.128 3269 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.02 % Favored : 92.82 % Rotamer: Outliers : 3.92 % Allowed : 27.71 % Favored : 68.37 % 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: -1.01 (0.23), residues: 1296 helix: 0.46 (0.23), residues: 483 sheet: -1.81 (0.37), residues: 180 loop : -1.16 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 196 TYR 0.018 0.002 TYR F 237 PHE 0.030 0.002 PHE h 6 TRP 0.008 0.001 TRP C 32 HIS 0.007 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (13611) covalent geometry : angle 0.65159 / 0.35 (18856) hydrogen bonds : bond 0.05247 / 4.95 ( 590) hydrogen bonds : angle 5.59921 / 7.12 ( 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: 46 poor density : 168 time to evaluate : 0.460 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: 0.8720 (OUTLIER) cc_final: 0.8510 (mm) REVERT: B 48 MET cc_start: 0.7533 (mmp) cc_final: 0.7208 (mmt) REVERT: B 76 LEU cc_start: 0.8535 (pp) cc_final: 0.8264 (mt) REVERT: D 255 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7288 (tp30) REVERT: E 5 TYR cc_start: 0.7171 (t80) cc_final: 0.6970 (t80) REVERT: F 242 ARG cc_start: 0.8780 (tpm170) cc_final: 0.8351 (tpm170) REVERT: h 55 LEU cc_start: 0.8666 (tp) cc_final: 0.8403 (tp) REVERT: i 21 GLU cc_start: 0.8106 (pm20) cc_final: 0.7805 (pm20) REVERT: l 78 MET cc_start: 0.7660 (tmm) cc_final: 0.7221 (tmm) REVERT: m 20 MET cc_start: 0.6370 (OUTLIER) cc_final: 0.5914 (mmt) REVERT: m 49 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.5854 (tt0) outliers start: 46 outliers final: 30 residues processed: 202 average time/residue: 0.1110 time to fit residues: 32.5474 Evaluate side-chains 190 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 123 VAL Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 197 GLU 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 F residue 64 HIS Chi-restraints excluded: chain F residue 75 MET 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 73 LEU 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 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 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: 9.9990 chunk 72 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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** ** 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** n 5 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.112785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.091288 restraints weight = 59738.837| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 4.62 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13611 Z= 0.159 Angle : 0.660 10.650 18856 Z= 0.348 Chirality : 0.042 0.254 2182 Planarity : 0.005 0.071 2015 Dihedral : 20.296 171.049 3269 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.87 % Favored : 92.98 % Rotamer: Outliers : 3.75 % Allowed : 28.05 % Favored : 68.20 % 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 (0.23), residues: 1296 helix: 0.56 (0.23), residues: 482 sheet: -1.74 (0.37), residues: 179 loop : -1.14 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG n 63 TYR 0.020 0.002 TYR F 237 PHE 0.032 0.002 PHE h 6 TRP 0.008 0.001 TRP C 32 HIS 0.010 0.001 HIS n 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (13611) covalent geometry : angle 0.66017 / 0.35 (18856) hydrogen bonds : bond 0.05104 / 4.81 ( 590) hydrogen bonds : angle 5.58278 / 7.16 ( 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 214 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 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 35 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8523 (mm) REVERT: B 76 LEU cc_start: 0.8634 (pp) cc_final: 0.8341 (mt) REVERT: D 255 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7334 (tp30) REVERT: E 5 TYR cc_start: 0.7197 (t80) cc_final: 0.6943 (t80) REVERT: F 242 ARG cc_start: 0.8767 (tpm170) cc_final: 0.8327 (tpm170) REVERT: h 55 LEU cc_start: 0.8657 (tp) cc_final: 0.8379 (tp) REVERT: i 21 GLU cc_start: 0.8046 (pm20) cc_final: 0.7785 (pm20) REVERT: k 16 ARG cc_start: 0.7291 (mpt180) cc_final: 0.6809 (mmt180) REVERT: k 17 MET cc_start: 0.6003 (mmm) cc_final: 0.5599 (mmm) REVERT: l 78 MET cc_start: 0.7234 (tmm) cc_final: 0.6523 (tmm) REVERT: m 20 MET cc_start: 0.6385 (OUTLIER) cc_final: 0.5784 (mmt) REVERT: m 49 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5704 (tt0) outliers start: 44 outliers final: 33 residues processed: 200 average time/residue: 0.1047 time to fit residues: 30.4457 Evaluate side-chains 196 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 123 VAL Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 46 ILE 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 F residue 64 HIS Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 166 ASP 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 73 LEU 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 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 44 GLU 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: 10.0000 chunk 16 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 78 optimal weight: 0.0980 chunk 3 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS F 260 GLN i 39 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.108909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.085648 restraints weight = 59662.464| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 4.73 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 13611 Z= 0.271 Angle : 0.763 9.989 18856 Z= 0.411 Chirality : 0.047 0.279 2182 Planarity : 0.006 0.064 2015 Dihedral : 20.551 171.279 3269 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.64 % Favored : 91.13 % Rotamer: Outliers : 4.26 % Allowed : 28.99 % Favored : 66.75 % 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: -1.33 (0.23), residues: 1296 helix: 0.09 (0.23), residues: 483 sheet: -1.82 (0.35), residues: 195 loop : -1.28 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 306 TYR 0.032 0.003 TYR F 237 PHE 0.037 0.003 PHE F 98 TRP 0.012 0.002 TRP C 32 HIS 0.015 0.002 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.27 (13611) covalent geometry : angle 0.76327 / 0.41 (18856) hydrogen bonds : bond 0.06659 / 6.39 ( 590) hydrogen bonds : angle 5.95480 / 7.61 ( 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 210 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 160 time to evaluate : 0.487 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: B 35 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8366 (mm) REVERT: B 48 MET cc_start: 0.7683 (mmp) cc_final: 0.7391 (mmt) REVERT: B 76 LEU cc_start: 0.8736 (pp) cc_final: 0.8418 (mt) REVERT: D 255 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7422 (tp30) REVERT: F 242 ARG cc_start: 0.8852 (tpm170) cc_final: 0.8309 (tpm170) REVERT: h 55 LEU cc_start: 0.8816 (tp) cc_final: 0.8519 (tp) REVERT: h 74 LEU cc_start: 0.3927 (OUTLIER) cc_final: 0.3705 (mm) REVERT: i 21 GLU cc_start: 0.8045 (pm20) cc_final: 0.7834 (pm20) REVERT: i 39 ASN cc_start: 0.6995 (OUTLIER) cc_final: 0.6765 (t0) REVERT: j 42 GLN cc_start: 0.4756 (OUTLIER) cc_final: 0.3027 (pt0) REVERT: k 47 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6890 (tm-30) REVERT: k 65 ARG cc_start: 0.7934 (mtm180) cc_final: 0.7624 (ptt180) REVERT: l 78 MET cc_start: 0.7458 (tmm) cc_final: 0.7126 (tmm) REVERT: m 20 MET cc_start: 0.6440 (OUTLIER) cc_final: 0.5991 (mmt) REVERT: m 30 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6684 (tmtt) REVERT: m 40 MET cc_start: 0.7209 (mpp) cc_final: 0.6844 (mtt) REVERT: m 49 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6211 (tt0) outliers start: 50 outliers final: 33 residues processed: 197 average time/residue: 0.1144 time to fit residues: 32.5005 Evaluate side-chains 194 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 B residue 70 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 29 ARG 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 352 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain h residue 32 VAL 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 39 ASN Chi-restraints excluded: chain i residue 67 LEU Chi-restraints excluded: chain j residue 37 ASP Chi-restraints excluded: chain j residue 42 GLN 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 43 CYS Chi-restraints excluded: chain k residue 47 GLU 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 20 MET Chi-restraints excluded: chain m residue 30 LYS 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 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: 0.8980 chunk 21 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 HIS ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS i 39 ASN ** 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 = 0.4410 r_free = 0.4410 target = 0.111574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.088532 restraints weight = 60372.327| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 4.94 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13611 Z= 0.148 Angle : 0.701 10.745 18856 Z= 0.369 Chirality : 0.044 0.259 2182 Planarity : 0.005 0.058 2015 Dihedral : 20.532 172.029 3269 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.17 % Favored : 93.67 % Rotamer: Outliers : 3.32 % Allowed : 29.84 % Favored : 66.84 % 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: -1.08 (0.23), residues: 1296 helix: 0.36 (0.23), residues: 483 sheet: -1.67 (0.36), residues: 189 loop : -1.21 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 306 TYR 0.031 0.002 TYR F 237 PHE 0.043 0.003 PHE F 98 TRP 0.012 0.001 TRP F 256 HIS 0.029 0.002 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (13611) covalent geometry : angle 0.70128 / 0.37 (18856) hydrogen bonds : bond 0.05030 / 4.77 ( 590) hydrogen bonds : angle 5.59417 / 7.19 ( 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 201 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.363 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: B 1 MET cc_start: 0.0064 (mtt) cc_final: -0.0282 (mmp) REVERT: B 35 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8384 (mm) REVERT: B 65 ASP cc_start: 0.8155 (m-30) cc_final: 0.7895 (t0) REVERT: B 76 LEU cc_start: 0.8675 (pp) cc_final: 0.8356 (mt) REVERT: D 255 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7431 (tp30) REVERT: F 242 ARG cc_start: 0.8836 (tpm170) cc_final: 0.8350 (tpm170) REVERT: h 55 LEU cc_start: 0.8752 (tp) cc_final: 0.8462 (tp) REVERT: h 74 LEU cc_start: 0.3861 (OUTLIER) cc_final: 0.3643 (mm) REVERT: i 21 GLU cc_start: 0.8080 (pm20) cc_final: 0.7860 (pm20) REVERT: j 42 GLN cc_start: 0.4523 (OUTLIER) cc_final: 0.2824 (pt0) REVERT: k 16 ARG cc_start: 0.7439 (mpt180) cc_final: 0.7117 (mmt180) REVERT: k 27 PHE cc_start: 0.8685 (t80) cc_final: 0.8353 (t80) REVERT: l 78 MET cc_start: 0.7443 (tmm) cc_final: 0.6993 (tmm) REVERT: m 20 MET cc_start: 0.6391 (OUTLIER) cc_final: 0.5965 (mmt) REVERT: m 30 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6507 (tmtt) REVERT: m 49 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.5779 (tt0) REVERT: m 55 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7885 (tt) outliers start: 39 outliers final: 26 residues processed: 190 average time/residue: 0.1010 time to fit residues: 28.2759 Evaluate side-chains 189 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 B residue 123 VAL Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 152 GLN 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 364 GLU 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 32 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 74 LEU 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 42 GLN Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 72 ILE 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 30 LYS Chi-restraints excluded: chain m residue 49 GLU Chi-restraints excluded: chain m residue 55 LEU 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: 4.9990 chunk 56 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS l 40 ASN ** l 83 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 = 0.4405 r_free = 0.4405 target = 0.111272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.088151 restraints weight = 60180.441| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 4.89 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 13611 Z= 0.158 Angle : 0.697 13.339 18856 Z= 0.363 Chirality : 0.043 0.261 2182 Planarity : 0.005 0.057 2015 Dihedral : 20.444 171.667 3269 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.10 % Favored : 92.75 % Rotamer: Outliers : 2.90 % Allowed : 30.52 % Favored : 66.58 % 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: -1.03 (0.23), residues: 1296 helix: 0.38 (0.23), residues: 483 sheet: -1.59 (0.36), residues: 187 loop : -1.19 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 306 TYR 0.030 0.002 TYR F 237 PHE 0.035 0.002 PHE j 70 TRP 0.008 0.001 TRP F 256 HIS 0.009 0.001 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (13611) covalent geometry : angle 0.69654 / 0.36 (18856) hydrogen bonds : bond 0.04959 / 4.67 ( 590) hydrogen bonds : angle 5.56585 / 7.14 ( 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 195 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.355 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 35 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8401 (mm) REVERT: B 65 ASP cc_start: 0.8164 (m-30) cc_final: 0.7895 (t0) REVERT: B 76 LEU cc_start: 0.8678 (pp) cc_final: 0.8358 (mt) REVERT: F 242 ARG cc_start: 0.8850 (tpm170) cc_final: 0.8413 (tpm170) REVERT: h 55 LEU cc_start: 0.8777 (tp) cc_final: 0.8487 (tp) REVERT: i 21 GLU cc_start: 0.8076 (pm20) cc_final: 0.7851 (pm20) REVERT: j 42 GLN cc_start: 0.4529 (OUTLIER) cc_final: 0.2836 (pt0) REVERT: k 16 ARG cc_start: 0.7473 (mpt180) cc_final: 0.7148 (mmt180) REVERT: l 78 MET cc_start: 0.7529 (tmm) cc_final: 0.7037 (tmm) REVERT: m 20 MET cc_start: 0.6326 (OUTLIER) cc_final: 0.5897 (mmt) REVERT: m 30 LYS cc_start: 0.6806 (OUTLIER) cc_final: 0.6452 (tmtt) REVERT: m 49 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5775 (tt0) REVERT: m 55 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7901 (tt) outliers start: 34 outliers final: 25 residues processed: 185 average time/residue: 0.1079 time to fit residues: 29.2514 Evaluate side-chains 191 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 B residue 123 VAL Chi-restraints excluded: chain C residue 29 ARG 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 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 i residue 67 LEU Chi-restraints excluded: chain j residue 37 ASP Chi-restraints excluded: chain j residue 42 GLN Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain l residue 40 ASN 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 30 LYS Chi-restraints excluded: chain m residue 49 GLU Chi-restraints excluded: chain m residue 55 LEU 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: 1.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS ** i 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 40 ASN ** 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 = 0.4406 r_free = 0.4406 target = 0.111292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.086644 restraints weight = 59874.694| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 4.60 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.219 13611 Z= 0.266 Angle : 1.071 59.195 18856 Z= 0.628 Chirality : 0.052 1.197 2182 Planarity : 0.005 0.057 2015 Dihedral : 20.450 171.665 3269 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.25 % Favored : 92.44 % Rotamer: Outliers : 2.81 % Allowed : 30.78 % Favored : 66.41 % Cbeta Deviations : 0.16 % 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: -1.05 (0.23), residues: 1296 helix: 0.35 (0.23), residues: 483 sheet: -1.59 (0.36), residues: 187 loop : -1.19 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG D 256 TYR 0.027 0.002 TYR F 237 PHE 0.033 0.002 PHE h 6 TRP 0.009 0.001 TRP C 32 HIS 0.008 0.001 HIS F 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.27 (13611) covalent geometry : angle 1.07090 / 0.63 (18856) hydrogen bonds : bond 0.04958 / 4.67 ( 590) hydrogen bonds : angle 5.56150 / 7.13 ( 1603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3085.97 seconds wall clock time: 53 minutes 47.03 seconds (3227.03 seconds total)