Starting phenix.real_space_refine on Thu May 15 09:51:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r7n_18984/05_2025/8r7n_18984.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r7n_18984/05_2025/8r7n_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_18984/05_2025/8r7n_18984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r7n_18984/05_2025/8r7n_18984.map" model { file = "/net/cci-nas-00/data/ceres_data/8r7n_18984/05_2025/8r7n_18984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r7n_18984/05_2025/8r7n_18984.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.71, per 1000 atoms: 0.66 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: 3.11 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 5.32 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: 4.55 Time building geometry restraints manager: 3.66 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=" CA LYS m 24 " pdb=" C LYS m 24 " ideal model delta sigma weight residual 1.523 1.495 0.027 1.41e-02 5.03e+03 3.80e+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: 6.770 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: 0.000 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.790 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 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= 0.208 Angle : 0.769 23.184 18856 Z= 0.406 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (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 TRP 0.010 0.001 TRP l 34 HIS 0.006 0.001 HIS l 65 PHE 0.034 0.002 PHE h 6 TYR 0.030 0.002 TYR F 237 ARG 0.024 0.001 ARG D 256 Details of bonding type rmsd hydrogen bonds : bond 0.23941 ( 590) hydrogen bonds : angle 8.48687 ( 1603) covalent geometry : bond 0.00562 (13611) covalent geometry : angle 0.76925 (18856) *********************** 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 : 1.352 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: 0.2641 time to fit residues: 66.4051 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 : 1.298 ------------------------------------------------------------------------------- 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 117 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN i 39 ASN j 40 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 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.115200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.090648 restraints weight = 59270.909| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 4.59 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 13611 Z= 0.155 Angle : 0.680 10.873 18856 Z= 0.352 Chirality : 0.042 0.205 2182 Planarity : 0.005 0.058 2015 Dihedral : 20.252 172.297 3271 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.10 % Favored : 93.75 % Rotamer: Outliers : 3.15 % Allowed : 24.13 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.23), residues: 1296 helix: 0.61 (0.23), residues: 482 sheet: -1.49 (0.37), residues: 178 loop : -1.07 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP l 34 HIS 0.008 0.001 HIS B 97 PHE 0.028 0.002 PHE F 98 TYR 0.019 0.002 TYR F 237 ARG 0.005 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.05813 ( 590) hydrogen bonds : angle 5.93394 ( 1603) covalent geometry : bond 0.00333 (13611) covalent geometry : angle 0.67960 (18856) *********************** 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 222 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 1.406 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 65 ASP cc_start: 0.8188 (t0) cc_final: 0.7935 (t70) REVERT: B 76 LEU cc_start: 0.8626 (mt) cc_final: 0.8382 (pp) REVERT: D 255 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7271 (tp30) REVERT: F 75 MET cc_start: 0.5455 (mmp) cc_final: 0.4891 (mmp) REVERT: F 242 ARG cc_start: 0.8726 (tpm170) cc_final: 0.8416 (tpm170) REVERT: h 55 LEU cc_start: 0.8639 (tp) cc_final: 0.8170 (tp) REVERT: l 78 MET cc_start: 0.7507 (tmm) cc_final: 0.7165 (tmm) outliers start: 37 outliers final: 18 residues processed: 210 average time/residue: 0.2654 time to fit residues: 81.3232 Evaluate side-chains 182 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain j residue 37 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain m residue 63 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 135 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN 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 ** l 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.115209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.090821 restraints weight = 60089.798| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 4.57 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13611 Z= 0.135 Angle : 0.637 10.937 18856 Z= 0.328 Chirality : 0.041 0.201 2182 Planarity : 0.005 0.060 2015 Dihedral : 20.136 171.563 3269 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.25 % Favored : 93.60 % Rotamer: Outliers : 3.41 % Allowed : 25.83 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.23), residues: 1296 helix: 0.57 (0.23), residues: 482 sheet: -1.48 (0.37), residues: 177 loop : -1.14 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 37 HIS 0.009 0.001 HIS n 5 PHE 0.025 0.002 PHE h 6 TYR 0.036 0.001 TYR F 237 ARG 0.007 0.000 ARG k 16 Details of bonding type rmsd hydrogen bonds : bond 0.05149 ( 590) hydrogen bonds : angle 5.57534 ( 1603) covalent geometry : bond 0.00285 (13611) covalent geometry : angle 0.63708 (18856) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 1.248 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: 0.8353 (mt) REVERT: B 65 ASP cc_start: 0.8248 (t0) cc_final: 0.7949 (t70) REVERT: B 76 LEU cc_start: 0.8735 (mt) cc_final: 0.8522 (pp) REVERT: D 255 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7176 (tp30) REVERT: F 75 MET cc_start: 0.5007 (mmp) cc_final: 0.4584 (mmp) REVERT: F 242 ARG cc_start: 0.8719 (tpm170) cc_final: 0.8433 (tpm170) REVERT: h 55 LEU cc_start: 0.8602 (tp) cc_final: 0.8241 (tp) REVERT: k 16 ARG cc_start: 0.7243 (mmt180) cc_final: 0.6995 (mmt180) REVERT: k 17 MET cc_start: 0.6397 (mmm) cc_final: 0.6159 (mmm) REVERT: l 78 MET cc_start: 0.7657 (tmm) cc_final: 0.7211 (tmm) REVERT: m 49 GLU cc_start: 0.6064 (OUTLIER) cc_final: 0.5301 (tt0) outliers start: 40 outliers final: 17 residues processed: 211 average time/residue: 0.2476 time to fit residues: 75.0454 Evaluate side-chains 178 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 40 VAL 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 F residue 64 HIS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain j residue 37 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain m residue 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 122 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 64 optimal weight: 50.0000 chunk 65 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 16 GLN ** l 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 67 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 = 0.4397 r_free = 0.4397 target = 0.110758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.087394 restraints weight = 59416.664| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 4.92 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13611 Z= 0.228 Angle : 0.710 12.460 18856 Z= 0.367 Chirality : 0.044 0.205 2182 Planarity : 0.005 0.061 2015 Dihedral : 20.365 171.714 3269 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.87 % Favored : 91.98 % Rotamer: Outliers : 5.20 % Allowed : 25.75 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.23), residues: 1296 helix: 0.30 (0.23), residues: 484 sheet: -1.81 (0.35), residues: 191 loop : -1.18 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 32 HIS 0.010 0.002 HIS C 120 PHE 0.026 0.003 PHE h 6 TYR 0.043 0.002 TYR F 237 ARG 0.008 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.06014 ( 590) hydrogen bonds : angle 5.75582 ( 1603) covalent geometry : bond 0.00493 (13611) covalent geometry : angle 0.71026 (18856) *********************** 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 230 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 169 time to evaluate : 1.387 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: 0.8729 (OUTLIER) cc_final: 0.8503 (mm) REVERT: B 65 ASP cc_start: 0.8431 (t0) cc_final: 0.8167 (m-30) REVERT: D 255 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7184 (tp30) REVERT: E 38 TYR cc_start: 0.7079 (m-80) cc_final: 0.6839 (m-80) REVERT: F 75 MET cc_start: 0.5308 (mmp) cc_final: 0.4819 (mmt) REVERT: F 80 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.7978 (tp) REVERT: F 242 ARG cc_start: 0.8717 (tpm170) cc_final: 0.8325 (tpm170) REVERT: F 266 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7644 (t0) REVERT: h 45 MET cc_start: 0.8148 (tmm) cc_final: 0.7925 (tmm) REVERT: h 55 LEU cc_start: 0.8781 (tp) cc_final: 0.8510 (tp) REVERT: i 21 GLU cc_start: 0.8117 (pm20) cc_final: 0.7810 (pm20) REVERT: j 83 LEU cc_start: 0.7782 (mt) cc_final: 0.7568 (mt) REVERT: k 17 MET cc_start: 0.6170 (mmm) cc_final: 0.5916 (mmm) REVERT: k 27 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8224 (t80) REVERT: l 78 MET cc_start: 0.7383 (tmm) cc_final: 0.6989 (tmm) REVERT: m 20 MET cc_start: 0.6342 (OUTLIER) cc_final: 0.5831 (mmt) REVERT: m 30 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6624 (tmtt) outliers start: 61 outliers final: 31 residues processed: 211 average time/residue: 0.2598 time to fit residues: 78.2994 Evaluate side-chains 195 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 70 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 40 VAL 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 352 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 266 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 79 ASN Chi-restraints excluded: chain k residue 27 PHE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 HIS ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 76 ASN l 40 ASN n 5 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.112741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.091967 restraints weight = 60363.586| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 4.80 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13611 Z= 0.142 Angle : 0.659 12.277 18856 Z= 0.334 Chirality : 0.042 0.195 2182 Planarity : 0.004 0.056 2015 Dihedral : 20.283 172.153 3269 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.17 % Favored : 93.67 % Rotamer: Outliers : 4.26 % Allowed : 26.85 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.23), residues: 1296 helix: 0.52 (0.23), residues: 484 sheet: -1.62 (0.38), residues: 176 loop : -1.16 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 32 HIS 0.007 0.001 HIS n 5 PHE 0.031 0.002 PHE j 70 TYR 0.024 0.002 TYR F 237 ARG 0.007 0.000 ARG k 16 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 590) hydrogen bonds : angle 5.44573 ( 1603) covalent geometry : bond 0.00303 (13611) covalent geometry : angle 0.65903 (18856) *********************** 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 232 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8510 (mm) REVERT: D 255 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7234 (tp30) REVERT: E 38 TYR cc_start: 0.6898 (m-80) cc_final: 0.6672 (m-80) REVERT: F 75 MET cc_start: 0.5011 (mmp) cc_final: 0.4458 (mmt) REVERT: F 242 ARG cc_start: 0.8653 (tpm170) cc_final: 0.8289 (tpm170) REVERT: F 266 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7526 (t0) REVERT: h 45 MET cc_start: 0.8139 (tmm) cc_final: 0.7843 (tmm) REVERT: h 55 LEU cc_start: 0.8714 (tp) cc_final: 0.8445 (tp) REVERT: i 21 GLU cc_start: 0.8049 (pm20) cc_final: 0.7748 (pm20) REVERT: k 27 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8056 (t80) REVERT: k 47 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6245 (tm-30) REVERT: k 65 ARG cc_start: 0.7984 (mtm180) cc_final: 0.7660 (ptp-170) REVERT: l 78 MET cc_start: 0.7162 (tmm) cc_final: 0.6385 (tmm) REVERT: m 20 MET cc_start: 0.6651 (OUTLIER) cc_final: 0.6030 (mmt) REVERT: m 49 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.5564 (tt0) outliers start: 50 outliers final: 28 residues processed: 217 average time/residue: 0.2566 time to fit residues: 79.6458 Evaluate side-chains 193 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain j residue 37 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 79 ASN Chi-restraints excluded: chain k residue 19 CYS Chi-restraints excluded: chain k residue 27 PHE Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 72 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 78 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 GLN ** i 39 ASN ** 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 = 0.4415 r_free = 0.4415 target = 0.111962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.087446 restraints weight = 60352.806| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 4.59 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13611 Z= 0.158 Angle : 0.666 12.687 18856 Z= 0.338 Chirality : 0.042 0.196 2182 Planarity : 0.005 0.054 2015 Dihedral : 20.231 171.580 3269 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.64 % Favored : 93.21 % Rotamer: Outliers : 3.84 % Allowed : 27.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.24), residues: 1296 helix: 0.59 (0.23), residues: 483 sheet: -1.56 (0.38), residues: 174 loop : -1.15 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 32 HIS 0.005 0.001 HIS E 30 PHE 0.029 0.002 PHE h 6 TYR 0.026 0.002 TYR F 237 ARG 0.007 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04828 ( 590) hydrogen bonds : angle 5.47328 ( 1603) covalent geometry : bond 0.00342 (13611) covalent geometry : angle 0.66594 (18856) *********************** 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 218 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 1.358 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: 0.8624 (OUTLIER) cc_final: 0.8362 (mm) REVERT: B 48 MET cc_start: 0.7472 (mmp) cc_final: 0.7261 (mmm) REVERT: B 65 ASP cc_start: 0.8185 (m-30) cc_final: 0.7942 (t0) REVERT: D 255 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7230 (tp30) REVERT: F 75 MET cc_start: 0.5152 (mmp) cc_final: 0.4349 (mmt) REVERT: F 242 ARG cc_start: 0.8737 (tpm170) cc_final: 0.8294 (tpm170) REVERT: F 266 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7676 (t0) REVERT: h 45 MET cc_start: 0.8059 (tmm) cc_final: 0.7851 (tmm) REVERT: h 55 LEU cc_start: 0.8751 (tp) cc_final: 0.8490 (tp) REVERT: i 21 GLU cc_start: 0.8123 (pm20) cc_final: 0.7892 (pm20) REVERT: k 17 MET cc_start: 0.5954 (mmm) cc_final: 0.5737 (mmm) REVERT: k 27 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7932 (t80) REVERT: l 78 MET cc_start: 0.7634 (tmm) cc_final: 0.7190 (tmm) REVERT: m 20 MET cc_start: 0.6434 (OUTLIER) cc_final: 0.5976 (mmt) REVERT: m 49 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.5879 (tt0) outliers start: 45 outliers final: 30 residues processed: 205 average time/residue: 0.2534 time to fit residues: 74.2075 Evaluate side-chains 192 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 40 VAL 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 364 GLU Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain i residue 67 LEU Chi-restraints excluded: chain j residue 37 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 79 ASN Chi-restraints excluded: chain k residue 19 CYS Chi-restraints excluded: chain k residue 27 PHE Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain l residue 84 ILE Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain m residue 19 VAL Chi-restraints excluded: chain m residue 20 MET Chi-restraints excluded: chain m residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 107 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 35 optimal weight: 0.0970 chunk 76 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 353 GLN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 HIS ** n 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.109845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.086585 restraints weight = 60266.835| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 4.80 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13611 Z= 0.198 Angle : 0.703 12.085 18856 Z= 0.361 Chirality : 0.044 0.235 2182 Planarity : 0.005 0.053 2015 Dihedral : 20.363 171.725 3269 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.25 % Favored : 92.59 % Rotamer: Outliers : 4.94 % Allowed : 28.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.24), residues: 1296 helix: 0.45 (0.23), residues: 484 sheet: -1.54 (0.37), residues: 188 loop : -1.14 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.011 0.002 HIS E 30 PHE 0.032 0.002 PHE h 6 TYR 0.025 0.002 TYR F 237 ARG 0.024 0.001 ARG D 356 Details of bonding type rmsd hydrogen bonds : bond 0.05342 ( 590) hydrogen bonds : angle 5.59535 ( 1603) covalent geometry : bond 0.00432 (13611) covalent geometry : angle 0.70336 (18856) *********************** 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 219 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 161 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.0225 (mtt) cc_final: -0.0012 (mmp) REVERT: B 35 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8359 (mm) REVERT: B 48 MET cc_start: 0.7715 (mmp) cc_final: 0.7461 (mmt) REVERT: B 65 ASP cc_start: 0.8197 (m-30) cc_final: 0.7943 (t0) REVERT: D 255 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7323 (tp30) REVERT: F 75 MET cc_start: 0.5241 (mmp) cc_final: 0.4961 (mmt) REVERT: F 242 ARG cc_start: 0.8767 (tpm170) cc_final: 0.8306 (tpm170) REVERT: h 17 ILE cc_start: 0.5160 (mt) cc_final: 0.4754 (mm) REVERT: h 55 LEU cc_start: 0.8890 (tp) cc_final: 0.8628 (tp) REVERT: h 63 ASN cc_start: 0.7705 (OUTLIER) cc_final: 0.7337 (p0) REVERT: i 21 GLU cc_start: 0.8114 (pm20) cc_final: 0.7803 (pm20) REVERT: j 42 GLN cc_start: 0.4515 (OUTLIER) cc_final: 0.2856 (pt0) REVERT: k 27 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8280 (t80) REVERT: k 47 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6506 (tm-30) REVERT: k 65 ARG cc_start: 0.8015 (mtm180) cc_final: 0.7600 (ptt180) REVERT: l 78 MET cc_start: 0.7463 (tmm) cc_final: 0.7062 (tmm) REVERT: m 20 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.5888 (mmt) REVERT: m 30 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.6535 (tmtt) REVERT: m 40 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6751 (mpp) REVERT: m 49 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6248 (tt0) outliers start: 58 outliers final: 35 residues processed: 202 average time/residue: 0.2629 time to fit residues: 75.7335 Evaluate side-chains 196 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 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 282 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 63 ASN 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 42 GLN Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 79 ASN Chi-restraints excluded: chain k residue 19 CYS Chi-restraints excluded: chain k residue 27 PHE Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain l residue 54 MET Chi-restraints excluded: chain l residue 77 ILE 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 30 LYS Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain m residue 40 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 44 GLU 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 49 optimal weight: 10.0000 chunk 105 optimal weight: 0.0970 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 86 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 HIS F 255 HIS ** i 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 67 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 = 0.4419 r_free = 0.4419 target = 0.112130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.089427 restraints weight = 59947.911| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 4.79 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13611 Z= 0.135 Angle : 0.689 12.029 18856 Z= 0.348 Chirality : 0.043 0.204 2182 Planarity : 0.004 0.055 2015 Dihedral : 20.196 171.867 3269 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.98 % Rotamer: Outliers : 3.92 % Allowed : 29.92 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.24), residues: 1296 helix: 0.59 (0.23), residues: 484 sheet: -1.46 (0.38), residues: 179 loop : -1.07 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP m 25 HIS 0.009 0.001 HIS E 30 PHE 0.033 0.002 PHE h 6 TYR 0.034 0.001 TYR F 237 ARG 0.015 0.000 ARG D 306 Details of bonding type rmsd hydrogen bonds : bond 0.04565 ( 590) hydrogen bonds : angle 5.31285 ( 1603) covalent geometry : bond 0.00288 (13611) covalent geometry : angle 0.68940 (18856) *********************** 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 223 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 177 time to evaluate : 1.238 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: 0.8630 (OUTLIER) cc_final: 0.8371 (mm) REVERT: B 65 ASP cc_start: 0.8120 (m-30) cc_final: 0.7861 (t0) REVERT: D 232 VAL cc_start: 0.6887 (OUTLIER) cc_final: 0.6602 (m) REVERT: F 242 ARG cc_start: 0.8770 (tpm170) cc_final: 0.8344 (tpm170) REVERT: F 266 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7647 (t0) REVERT: h 17 ILE cc_start: 0.4942 (mt) cc_final: 0.4524 (mm) REVERT: h 55 LEU cc_start: 0.8822 (tp) cc_final: 0.8587 (tp) REVERT: i 21 GLU cc_start: 0.8138 (pm20) cc_final: 0.7830 (pm20) REVERT: j 42 GLN cc_start: 0.4301 (OUTLIER) cc_final: 0.2627 (pt0) REVERT: k 27 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.8104 (t80) REVERT: k 47 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6681 (tm-30) REVERT: k 65 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7641 (ptt180) REVERT: l 78 MET cc_start: 0.7469 (tmm) cc_final: 0.7076 (tmm) REVERT: m 20 MET cc_start: 0.6492 (OUTLIER) cc_final: 0.6024 (mmt) REVERT: m 30 LYS cc_start: 0.6598 (OUTLIER) cc_final: 0.6279 (tmtt) REVERT: m 40 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.6746 (mpp) REVERT: m 49 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5932 (tm-30) REVERT: m 55 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7848 (tt) REVERT: n 13 MET cc_start: 0.7319 (tpp) cc_final: 0.6961 (tpp) outliers start: 46 outliers final: 24 residues processed: 210 average time/residue: 0.2640 time to fit residues: 79.0341 Evaluate side-chains 198 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 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 301 VAL Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain h residue 32 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 79 ASN Chi-restraints excluded: chain k residue 19 CYS Chi-restraints excluded: chain k residue 27 PHE Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 65 ARG 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 40 MET Chi-restraints excluded: chain m residue 49 GLU Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 63 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 255 HIS ** i 39 ASN ** 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 ** n 22 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 = 0.4404 r_free = 0.4404 target = 0.111288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.086984 restraints weight = 59935.053| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 4.58 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13611 Z= 0.149 Angle : 0.694 11.689 18856 Z= 0.351 Chirality : 0.042 0.220 2182 Planarity : 0.004 0.061 2015 Dihedral : 20.114 171.334 3269 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.94 % Favored : 93.90 % Rotamer: Outliers : 3.58 % Allowed : 30.01 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.24), residues: 1296 helix: 0.61 (0.23), residues: 484 sheet: -1.43 (0.38), residues: 179 loop : -1.06 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 256 HIS 0.018 0.001 HIS F 255 PHE 0.031 0.002 PHE h 6 TYR 0.022 0.001 TYR F 237 ARG 0.011 0.000 ARG D 306 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 590) hydrogen bonds : angle 5.31253 ( 1603) covalent geometry : bond 0.00325 (13611) covalent geometry : angle 0.69353 (18856) *********************** 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 212 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 1.299 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: 0.8615 (OUTLIER) cc_final: 0.8339 (mm) REVERT: B 65 ASP cc_start: 0.8168 (m-30) cc_final: 0.7901 (t0) REVERT: D 232 VAL cc_start: 0.7094 (OUTLIER) cc_final: 0.6805 (m) REVERT: F 242 ARG cc_start: 0.8889 (tpm170) cc_final: 0.8351 (tpm170) REVERT: h 17 ILE cc_start: 0.5075 (mt) cc_final: 0.4775 (mm) REVERT: h 55 LEU cc_start: 0.9055 (tp) cc_final: 0.8706 (tp) REVERT: i 21 GLU cc_start: 0.8159 (pm20) cc_final: 0.7885 (pm20) REVERT: j 42 GLN cc_start: 0.4361 (OUTLIER) cc_final: 0.2744 (pt0) REVERT: k 27 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7882 (t80) REVERT: k 47 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6513 (tm-30) REVERT: k 65 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7636 (ptt180) REVERT: l 78 MET cc_start: 0.7670 (tmm) cc_final: 0.7230 (tmm) REVERT: m 20 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.6054 (mmt) REVERT: m 30 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.6227 (tmtt) REVERT: m 40 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6786 (mpp) REVERT: m 49 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5623 (tt0) REVERT: m 55 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7874 (tt) outliers start: 42 outliers final: 25 residues processed: 199 average time/residue: 0.2535 time to fit residues: 72.0819 Evaluate side-chains 197 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain h residue 32 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 j residue 79 ASN Chi-restraints excluded: chain k residue 19 CYS Chi-restraints excluded: chain k residue 27 PHE Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 65 ARG 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 30 LYS Chi-restraints excluded: chain m residue 40 MET Chi-restraints excluded: chain m residue 49 GLU Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 63 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 73 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 74 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 111 optimal weight: 0.1980 chunk 2 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 255 HIS h 12 HIS h 39 HIS ** i 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.112134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.089556 restraints weight = 59911.617| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 4.80 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13611 Z= 0.135 Angle : 0.702 12.088 18856 Z= 0.353 Chirality : 0.042 0.258 2182 Planarity : 0.004 0.063 2015 Dihedral : 20.019 171.212 3269 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.63 % Favored : 94.21 % Rotamer: Outliers : 3.15 % Allowed : 30.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1296 helix: 0.72 (0.23), residues: 483 sheet: -1.29 (0.37), residues: 199 loop : -1.02 (0.27), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 32 HIS 0.032 0.002 HIS F 255 PHE 0.033 0.002 PHE h 6 TYR 0.011 0.001 TYR E 9 ARG 0.012 0.000 ARG D 306 Details of bonding type rmsd hydrogen bonds : bond 0.04486 ( 590) hydrogen bonds : angle 5.19411 ( 1603) covalent geometry : bond 0.00292 (13611) covalent geometry : angle 0.70208 (18856) ********************** 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 210 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 1.259 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: symmetry clash REVERT: B 35 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8369 (mm) REVERT: B 65 ASP cc_start: 0.8114 (m-30) cc_final: 0.7861 (t0) REVERT: B 75 GLN cc_start: 0.8793 (mt0) cc_final: 0.8427 (mt0) REVERT: F 75 MET cc_start: 0.5824 (mmt) cc_final: 0.5387 (mmp) REVERT: F 242 ARG cc_start: 0.8913 (tpm170) cc_final: 0.8452 (tpm170) REVERT: h 17 ILE cc_start: 0.5177 (mt) cc_final: 0.4788 (mm) REVERT: h 55 LEU cc_start: 0.9055 (tp) cc_final: 0.8712 (tp) REVERT: i 21 GLU cc_start: 0.8152 (pm20) cc_final: 0.7865 (pm20) REVERT: j 42 GLN cc_start: 0.4278 (OUTLIER) cc_final: 0.2652 (pt0) REVERT: k 27 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8036 (t80) REVERT: k 47 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6670 (tm-30) REVERT: k 65 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7606 (ptt180) REVERT: k 80 MET cc_start: 0.8341 (tmm) cc_final: 0.7927 (tmm) REVERT: l 78 MET cc_start: 0.7462 (tmm) cc_final: 0.7008 (tmm) REVERT: m 20 MET cc_start: 0.6435 (OUTLIER) cc_final: 0.5983 (mmt) REVERT: m 30 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.6257 (tmtt) REVERT: m 40 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6808 (mpp) REVERT: m 49 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5522 (tt0) REVERT: m 55 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7835 (tt) outliers start: 37 outliers final: 24 residues processed: 195 average time/residue: 0.2631 time to fit residues: 72.6994 Evaluate side-chains 200 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain h residue 32 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 79 ASN Chi-restraints excluded: chain k residue 19 CYS Chi-restraints excluded: chain k residue 27 PHE Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain k residue 47 GLU Chi-restraints excluded: chain k residue 65 ARG Chi-restraints excluded: chain l residue 54 MET 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 40 MET Chi-restraints excluded: chain m residue 49 GLU Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 63 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 91 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 35 optimal weight: 0.2980 chunk 73 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 chunk 7 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 255 HIS i 39 ASN ** m 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 HIS ** n 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.112214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.089598 restraints weight = 59880.163| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 4.89 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13611 Z= 0.135 Angle : 0.695 11.873 18856 Z= 0.349 Chirality : 0.042 0.309 2182 Planarity : 0.004 0.063 2015 Dihedral : 19.942 171.052 3269 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.79 % Favored : 94.06 % Rotamer: Outliers : 3.24 % Allowed : 30.69 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1296 helix: 0.77 (0.23), residues: 483 sheet: -1.13 (0.36), residues: 201 loop : -1.01 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 32 HIS 0.015 0.001 HIS F 255 PHE 0.033 0.002 PHE h 6 TYR 0.014 0.001 TYR h 67 ARG 0.010 0.000 ARG D 306 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 590) hydrogen bonds : angle 5.15225 ( 1603) covalent geometry : bond 0.00293 (13611) covalent geometry : angle 0.69525 (18856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6935.47 seconds wall clock time: 121 minutes 6.13 seconds (7266.13 seconds total)