Starting phenix.real_space_refine on Wed Jun 11 16:20:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r7n_18984/06_2025/8r7n_18984.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r7n_18984/06_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_18984/06_2025/8r7n_18984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r7n_18984/06_2025/8r7n_18984.map" model { file = "/net/cci-nas-00/data/ceres_data/8r7n_18984/06_2025/8r7n_18984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r7n_18984/06_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-5710/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: 9.33, per 1000 atoms: 0.71 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: 3.27 Conformation dependent library (CDL) restraints added in 1.5 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: 4.97 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: 4.12 Time building geometry restraints manager: 3.86 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: 93.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.130 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.790 ------------------------------------------------------------------------------- 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 : 1.463 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: 0.2962 time to fit residues: 73.9187 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 : 1.451 ------------------------------------------------------------------------------- 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 = 58)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.090818 restraints weight = 59271.181| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 4.52 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.1155 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 : 20.252 172.296 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 0.05812 ( 590) hydrogen bonds : angle 5.93382 ( 1603) covalent geometry : bond 0.00333 (13611) covalent geometry : angle 0.67962 (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 : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 ASP cc_start: 0.8206 (t0) cc_final: 0.7951 (t70) REVERT: B 76 LEU cc_start: 0.8640 (mt) cc_final: 0.8387 (pp) REVERT: D 255 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7248 (tp30) REVERT: F 75 MET cc_start: 0.5316 (mmp) cc_final: 0.4736 (mmp) REVERT: F 242 ARG cc_start: 0.8732 (tpm170) cc_final: 0.8418 (tpm170) REVERT: h 55 LEU cc_start: 0.8637 (tp) cc_final: 0.8172 (tp) REVERT: l 78 MET cc_start: 0.7510 (tmm) cc_final: 0.7181 (tmm) outliers start: 37 outliers final: 18 residues processed: 210 average time/residue: 0.2557 time to fit residues: 77.1848 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 : 1.297 ------------------------------------------------------------------------------- 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: 0.9990 chunk 34 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 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 = 0.4447 r_free = 0.4447 target = 0.114703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.090199 restraints weight = 60308.695| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 4.61 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13611 Z= 0.143 Angle : 0.641 10.913 18856 Z= 0.330 Chirality : 0.041 0.201 2182 Planarity : 0.005 0.059 2015 Dihedral : 20.161 171.650 3269 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.64 % Favored : 93.21 % Rotamer: Outliers : 3.92 % Allowed : 25.40 % Favored : 70.67 % 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: -0.88 (0.23), residues: 1296 helix: 0.55 (0.23), residues: 482 sheet: -1.52 (0.37), residues: 177 loop : -1.15 (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 0.05265 ( 590) hydrogen bonds : angle 5.62053 ( 1603) covalent geometry : bond 0.00303 (13611) covalent geometry : angle 0.64100 (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 225 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8360 (mt) REVERT: B 65 ASP cc_start: 0.8268 (t0) cc_final: 0.7969 (t70) REVERT: B 76 LEU cc_start: 0.8768 (mt) cc_final: 0.8542 (pp) REVERT: D 255 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: F 75 MET cc_start: 0.5018 (mmp) cc_final: 0.4588 (mmp) REVERT: F 242 ARG cc_start: 0.8728 (tpm170) cc_final: 0.8465 (tpm170) REVERT: h 55 LEU cc_start: 0.8620 (tp) cc_final: 0.8259 (tp) REVERT: k 16 ARG cc_start: 0.7251 (mmt180) cc_final: 0.7004 (mmt180) REVERT: k 17 MET cc_start: 0.6407 (mmm) cc_final: 0.6157 (mmm) REVERT: l 78 MET cc_start: 0.7641 (tmm) cc_final: 0.7223 (tmm) REVERT: m 49 GLU cc_start: 0.6099 (OUTLIER) cc_final: 0.5348 (tt0) outliers start: 46 outliers final: 22 residues processed: 212 average time/residue: 0.2637 time to fit residues: 79.7412 Evaluate side-chains 182 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 282 VAL Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain F residue 64 HIS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain j residue 37 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 43 CYS Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain m residue 49 GLU Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 48 MET Chi-restraints excluded: chain n residue 60 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 122 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 64 optimal weight: 50.0000 chunk 65 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 89 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN ** F 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 39 ASN ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.114233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.089815 restraints weight = 59082.197| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 4.51 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1894 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= 0.148 Angle : 0.633 10.516 18856 Z= 0.325 Chirality : 0.041 0.243 2182 Planarity : 0.004 0.056 2015 Dihedral : 20.137 171.368 3269 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.33 % Favored : 93.52 % Rotamer: Outliers : 4.18 % Allowed : 24.89 % Favored : 70.93 % 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: -0.88 (0.23), residues: 1296 helix: 0.59 (0.23), residues: 483 sheet: -1.69 (0.36), residues: 183 loop : -1.11 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 32 HIS 0.004 0.001 HIS E 30 PHE 0.026 0.002 PHE h 6 TYR 0.038 0.002 TYR F 237 ARG 0.005 0.000 ARG n 63 Details of bonding type rmsd hydrogen bonds : bond 0.04939 ( 590) hydrogen bonds : angle 5.46645 ( 1603) covalent geometry : bond 0.00318 (13611) covalent geometry : angle 0.63264 (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 225 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 1.315 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: 0.8744 (OUTLIER) cc_final: 0.8532 (mm) REVERT: B 65 ASP cc_start: 0.8306 (t0) cc_final: 0.8068 (m-30) REVERT: D 255 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7132 (tp30) REVERT: D 352 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6405 (tt) REVERT: F 75 MET cc_start: 0.4973 (mmp) cc_final: 0.4479 (mmp) REVERT: F 117 GLN cc_start: 0.7947 (tt0) cc_final: 0.7668 (tm-30) REVERT: F 242 ARG cc_start: 0.8721 (tpm170) cc_final: 0.8343 (tpm170) REVERT: h 55 LEU cc_start: 0.8619 (tp) cc_final: 0.8265 (tp) REVERT: k 16 ARG cc_start: 0.7199 (mmt180) cc_final: 0.6870 (mmt180) REVERT: k 17 MET cc_start: 0.6431 (mmm) cc_final: 0.6158 (mmm) REVERT: k 27 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7867 (t80) REVERT: l 78 MET cc_start: 0.7686 (tmm) cc_final: 0.7269 (tmm) REVERT: m 20 MET cc_start: 0.6390 (OUTLIER) cc_final: 0.5938 (mmt) REVERT: m 49 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5605 (tt0) REVERT: n 70 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6441 (pp) outliers start: 49 outliers final: 28 residues processed: 205 average time/residue: 0.2649 time to fit residues: 77.9465 Evaluate side-chains 192 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 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 1 MET 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 h residue 32 VAL Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain i residue 33 THR Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain 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 84 ILE Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain m residue 19 VAL Chi-restraints excluded: chain m residue 20 MET Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain m residue 49 GLU Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 48 MET Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 70 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 0.0470 chunk 125 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 115 optimal weight: 0.4980 chunk 10 optimal weight: 7.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- 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** ** j 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.113955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.089499 restraints weight = 59739.389| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 4.60 r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13611 Z= 0.146 Angle : 0.638 11.121 18856 Z= 0.327 Chirality : 0.040 0.190 2182 Planarity : 0.004 0.061 2015 Dihedral : 20.122 171.210 3269 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.33 % Favored : 93.52 % Rotamer: Outliers : 4.26 % Allowed : 25.75 % Favored : 69.99 % 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: -0.84 (0.23), residues: 1296 helix: 0.61 (0.23), residues: 484 sheet: -1.55 (0.37), residues: 176 loop : -1.15 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 32 HIS 0.008 0.001 HIS n 5 PHE 0.027 0.002 PHE h 6 TYR 0.013 0.001 TYR h 67 ARG 0.006 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04789 ( 590) hydrogen bonds : angle 5.40685 ( 1603) covalent geometry : bond 0.00314 (13611) covalent geometry : angle 0.63833 (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 233 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 1.410 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: 0.8737 (OUTLIER) cc_final: 0.8518 (mm) REVERT: B 76 LEU cc_start: 0.8515 (pp) cc_final: 0.8193 (mt) REVERT: C 128 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8723 (mm) REVERT: D 255 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7124 (tp30) REVERT: F 75 MET cc_start: 0.5149 (mmp) cc_final: 0.4618 (mmp) REVERT: F 117 GLN cc_start: 0.7952 (tt0) cc_final: 0.7665 (tm-30) REVERT: F 242 ARG cc_start: 0.8760 (tpm170) cc_final: 0.8405 (tpm170) REVERT: h 55 LEU cc_start: 0.8645 (tp) cc_final: 0.8385 (tp) REVERT: k 16 ARG cc_start: 0.7156 (mmt180) cc_final: 0.6936 (mmt180) REVERT: k 17 MET cc_start: 0.6386 (mmm) cc_final: 0.5940 (mmm) REVERT: k 27 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7924 (t80) REVERT: k 83 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7501 (tm-30) REVERT: l 78 MET cc_start: 0.7676 (tmm) cc_final: 0.7242 (tmm) REVERT: m 20 MET cc_start: 0.6403 (OUTLIER) cc_final: 0.5930 (mmt) REVERT: m 49 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5671 (tt0) REVERT: n 70 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6456 (pp) outliers start: 50 outliers final: 29 residues processed: 216 average time/residue: 0.2534 time to fit residues: 78.9987 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 : 1.442 ------------------------------------------------------------------------------- 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 C residue 128 LEU 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 364 GLU 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 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 63 ILE 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 48 MET Chi-restraints excluded: chain n residue 60 VAL Chi-restraints excluded: chain n residue 70 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 78 optimal weight: 0.8980 chunk 115 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN ** F 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 40 ASN ** 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 = 0.4432 r_free = 0.4432 target = 0.112946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.088648 restraints weight = 60202.151| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 4.56 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13611 Z= 0.154 Angle : 0.652 10.314 18856 Z= 0.334 Chirality : 0.041 0.192 2182 Planarity : 0.004 0.059 2015 Dihedral : 20.122 171.093 3269 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.10 % Favored : 92.75 % Rotamer: Outliers : 5.03 % Allowed : 25.83 % Favored : 69.14 % 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: -0.83 (0.24), residues: 1296 helix: 0.58 (0.23), residues: 483 sheet: -1.53 (0.38), residues: 176 loop : -1.11 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 32 HIS 0.010 0.001 HIS F 255 PHE 0.038 0.002 PHE F 98 TYR 0.015 0.001 TYR m 71 ARG 0.006 0.000 ARG n 63 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 590) hydrogen bonds : angle 5.30244 ( 1603) covalent geometry : bond 0.00332 (13611) covalent geometry : angle 0.65239 (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 235 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 176 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8446 (mm) REVERT: B 65 ASP cc_start: 0.8153 (m-30) cc_final: 0.7881 (t0) REVERT: B 76 LEU cc_start: 0.8543 (pp) cc_final: 0.8246 (mt) REVERT: D 255 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7193 (tp30) REVERT: F 75 MET cc_start: 0.4934 (mmp) cc_final: 0.4185 (mmt) REVERT: F 242 ARG cc_start: 0.8866 (tpm170) cc_final: 0.8412 (tpm170) REVERT: h 55 LEU cc_start: 0.8706 (tp) cc_final: 0.8445 (tp) REVERT: k 16 ARG cc_start: 0.7191 (mmt180) cc_final: 0.6815 (mmt180) REVERT: k 17 MET cc_start: 0.6324 (mmm) cc_final: 0.6034 (mmm) REVERT: k 27 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7901 (t80) REVERT: k 47 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6237 (tm-30) REVERT: l 78 MET cc_start: 0.7635 (tmm) cc_final: 0.7163 (tmm) REVERT: m 20 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.5931 (mmt) REVERT: m 30 LYS cc_start: 0.6616 (OUTLIER) cc_final: 0.6308 (tmtt) REVERT: m 49 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5831 (tt0) outliers start: 59 outliers final: 34 residues processed: 218 average time/residue: 0.2559 time to fit residues: 80.3659 Evaluate side-chains 199 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 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 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 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 63 ILE 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 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 49 GLU Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain n residue 48 MET Chi-restraints excluded: chain n residue 60 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 107 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 85 optimal weight: 0.3980 chunk 136 optimal weight: 1.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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** E 20 ASN ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 HIS ** k 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 16 GLN ** m 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.113542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.089415 restraints weight = 60461.352| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 4.57 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13611 Z= 0.139 Angle : 0.672 12.177 18856 Z= 0.340 Chirality : 0.042 0.193 2182 Planarity : 0.005 0.063 2015 Dihedral : 20.082 170.994 3269 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.25 % Favored : 93.60 % Rotamer: Outliers : 4.18 % Allowed : 27.54 % Favored : 68.29 % 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: -0.74 (0.24), residues: 1296 helix: 0.64 (0.23), residues: 484 sheet: -1.28 (0.39), residues: 174 loop : -1.11 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 32 HIS 0.009 0.001 HIS F 255 PHE 0.031 0.002 PHE h 6 TYR 0.012 0.001 TYR h 67 ARG 0.011 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 590) hydrogen bonds : angle 5.26958 ( 1603) covalent geometry : bond 0.00297 (13611) covalent geometry : angle 0.67220 (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 217 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8889 (mt) REVERT: B 65 ASP cc_start: 0.8127 (m-30) cc_final: 0.7843 (t0) REVERT: B 76 LEU cc_start: 0.8563 (pp) cc_final: 0.8278 (mt) REVERT: D 232 VAL cc_start: 0.6986 (OUTLIER) cc_final: 0.6685 (m) REVERT: D 306 ARG cc_start: 0.8786 (ptp-170) cc_final: 0.8576 (ptp-170) REVERT: F 242 ARG cc_start: 0.8917 (tpm170) cc_final: 0.8461 (tpm170) REVERT: h 55 LEU cc_start: 0.8712 (tp) cc_final: 0.8443 (tp) REVERT: j 42 GLN cc_start: 0.4453 (OUTLIER) cc_final: 0.2798 (pt0) REVERT: k 16 ARG cc_start: 0.7088 (mmt180) cc_final: 0.6802 (mmt180) REVERT: k 17 MET cc_start: 0.6298 (mmm) cc_final: 0.5921 (mmm) REVERT: k 27 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7952 (t80) REVERT: k 47 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6325 (tm-30) REVERT: l 78 MET cc_start: 0.7668 (tmm) cc_final: 0.7179 (tmm) REVERT: m 20 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.5937 (mmt) REVERT: m 30 LYS cc_start: 0.6577 (OUTLIER) cc_final: 0.6267 (tmtt) REVERT: m 40 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6826 (mpp) REVERT: m 49 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5656 (tt0) outliers start: 49 outliers final: 32 residues processed: 202 average time/residue: 0.2477 time to fit residues: 73.3090 Evaluate side-chains 198 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 64 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 197 GLU Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 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 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 42 GLN Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 63 ILE 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 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 63 LEU Chi-restraints excluded: chain n residue 9 LEU Chi-restraints excluded: chain n residue 19 LEU Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain n residue 48 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.2225 > 50: distance: 68 - 73: 21.610 distance: 73 - 74: 11.105 distance: 74 - 75: 50.911 distance: 74 - 77: 25.990 distance: 75 - 76: 39.946 distance: 75 - 81: 35.033 distance: 77 - 78: 37.148 distance: 77 - 79: 29.010 distance: 78 - 80: 43.042 distance: 81 - 82: 59.846 distance: 82 - 83: 63.245 distance: 82 - 85: 59.528 distance: 83 - 84: 51.979 distance: 83 - 89: 40.204 distance: 85 - 86: 36.599 distance: 86 - 87: 34.285 distance: 86 - 88: 32.607 distance: 89 - 90: 52.139 distance: 89 - 95: 64.261 distance: 90 - 91: 35.174 distance: 90 - 93: 28.282 distance: 91 - 92: 29.693 distance: 91 - 96: 41.488 distance: 92 - 112: 5.911 distance: 93 - 94: 21.404 distance: 94 - 95: 48.580 distance: 96 - 97: 51.759 distance: 97 - 98: 20.522 distance: 97 - 100: 31.051 distance: 98 - 99: 50.833 distance: 98 - 104: 34.744 distance: 100 - 101: 24.484 distance: 101 - 102: 47.762 distance: 104 - 105: 23.310 distance: 105 - 106: 25.380 distance: 106 - 107: 13.443 distance: 106 - 112: 31.672 distance: 107 - 129: 33.267 distance: 109 - 110: 29.948 distance: 110 - 111: 4.019 distance: 112 - 113: 15.705 distance: 113 - 114: 20.016 distance: 113 - 116: 18.805 distance: 114 - 115: 32.075 distance: 114 - 120: 40.767 distance: 115 - 137: 36.450 distance: 116 - 117: 22.099 distance: 117 - 118: 18.583 distance: 117 - 119: 16.238 distance: 120 - 121: 34.510 distance: 121 - 122: 43.711 distance: 121 - 124: 40.408 distance: 122 - 123: 24.333 distance: 122 - 129: 7.848 distance: 124 - 125: 14.806 distance: 125 - 126: 34.082 distance: 126 - 127: 37.445 distance: 127 - 128: 50.572 distance: 129 - 130: 15.362 distance: 130 - 131: 14.932 distance: 130 - 133: 20.495 distance: 131 - 132: 27.104 distance: 131 - 137: 18.864 distance: 133 - 134: 13.397 distance: 134 - 135: 45.688 distance: 134 - 136: 38.836 distance: 137 - 138: 33.245 distance: 138 - 139: 63.823 distance: 139 - 140: 65.935 distance: 139 - 142: 63.490 distance: 142 - 143: 10.177 distance: 142 - 148: 39.693 distance: 143 - 144: 19.681 distance: 143 - 146: 9.476 distance: 144 - 145: 25.747 distance: 144 - 149: 28.516 distance: 146 - 147: 6.972 distance: 147 - 148: 44.406