Starting phenix.real_space_refine on Sun Apr 5 20:05:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7egf_31115/04_2026/7egf_31115.cif Found real_map, /net/cci-nas-00/data/ceres_data/7egf_31115/04_2026/7egf_31115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7egf_31115/04_2026/7egf_31115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7egf_31115/04_2026/7egf_31115.map" model { file = "/net/cci-nas-00/data/ceres_data/7egf_31115/04_2026/7egf_31115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7egf_31115/04_2026/7egf_31115.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.065 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: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 8448 2.51 5 N 2316 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13303 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1412 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain: "c" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1011 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 118} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "d" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1307 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 155} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "e" Number of atoms: 4327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4327 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 516} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "f" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1135 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "i" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 108} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "j" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 759 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain breaks: 1 Chain: "k" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 785 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "l" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 876 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "m" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 724 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Time building chain proxies: 2.95, per 1000 atoms: 0.22 Number of scatterers: 13303 At special positions: 0 Unit cell: (103.39, 138.205, 136.095, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 2470 8.00 N 2316 7.00 C 8448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 592.2 milliseconds 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3146 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 14 sheets defined 44.9% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'P' and resid 179 through 187 removed outlier: 4.049A pdb=" N ILE P 183 " --> pdb=" O ASP P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 243 Processing helix chain 'P' and resid 269 through 277 removed outlier: 3.834A pdb=" N LEU P 273 " --> pdb=" O ARG P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 335 removed outlier: 3.972A pdb=" N ILE P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Proline residue: P 330 - end of helix Processing helix chain 'c' and resid 2 through 16 Processing helix chain 'c' and resid 16 through 21 removed outlier: 3.552A pdb=" N ALA c 20 " --> pdb=" O GLN c 16 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU c 21 " --> pdb=" O ILE c 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 16 through 21' Processing helix chain 'c' and resid 28 through 56 removed outlier: 3.562A pdb=" N HIS c 32 " --> pdb=" O LEU c 28 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU c 33 " --> pdb=" O SER c 29 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU c 34 " --> pdb=" O ALA c 30 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP c 36 " --> pdb=" O HIS c 32 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN c 43 " --> pdb=" O GLN c 39 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER c 53 " --> pdb=" O CYS c 49 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR c 56 " --> pdb=" O TYR c 52 " (cutoff:3.500A) Processing helix chain 'c' and resid 62 through 74 removed outlier: 3.935A pdb=" N GLN c 71 " --> pdb=" O GLY c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 76 through 87 removed outlier: 3.607A pdb=" N GLU c 81 " --> pdb=" O LEU c 77 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP c 82 " --> pdb=" O HIS c 78 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN c 86 " --> pdb=" O ASP c 82 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE c 87 " --> pdb=" O TYR c 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 844 through 849 removed outlier: 3.515A pdb=" N GLU d 848 " --> pdb=" O ASN d 844 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER d 849 " --> pdb=" O LEU d 845 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 844 through 849' Processing helix chain 'd' and resid 849 through 855 removed outlier: 4.155A pdb=" N LEU d 853 " --> pdb=" O SER d 849 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR d 855 " --> pdb=" O ARG d 851 " (cutoff:3.500A) Processing helix chain 'd' and resid 856 through 858 No H-bonds generated for 'chain 'd' and resid 856 through 858' Processing helix chain 'd' and resid 874 through 885 removed outlier: 3.676A pdb=" N ARG d 880 " --> pdb=" O ALA d 876 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU d 883 " --> pdb=" O GLN d 879 " (cutoff:3.500A) Processing helix chain 'd' and resid 898 through 922 removed outlier: 3.548A pdb=" N HIS d 904 " --> pdb=" O SER d 900 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN d 907 " --> pdb=" O SER d 903 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU d 913 " --> pdb=" O ARG d 909 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU d 919 " --> pdb=" O GLU d 915 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR d 920 " --> pdb=" O LYS d 916 " (cutoff:3.500A) Processing helix chain 'd' and resid 923 through 926 Processing helix chain 'd' and resid 939 through 968 Processing helix chain 'd' and resid 1059 through 1069 removed outlier: 3.754A pdb=" N LEU d1063 " --> pdb=" O ASN d1059 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS d1066 " --> pdb=" O ASP d1062 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN d1069 " --> pdb=" O PHE d1065 " (cutoff:3.500A) Processing helix chain 'd' and resid 1076 through 1083 removed outlier: 3.688A pdb=" N TYR d1080 " --> pdb=" O SER d1076 " (cutoff:3.500A) Processing helix chain 'e' and resid 213 through 228 Processing helix chain 'e' and resid 229 through 255 removed outlier: 4.511A pdb=" N ALA e 234 " --> pdb=" O ASP e 230 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU e 235 " --> pdb=" O CYS e 231 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN e 238 " --> pdb=" O ALA e 234 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU e 239 " --> pdb=" O GLU e 235 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE e 240 " --> pdb=" O LEU e 236 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR e 241 " --> pdb=" O SER e 237 " (cutoff:3.500A) Proline residue: e 242 - end of helix Processing helix chain 'e' and resid 256 through 268 Processing helix chain 'e' and resid 276 through 285 Processing helix chain 'e' and resid 287 through 292 removed outlier: 3.906A pdb=" N MET e 291 " --> pdb=" O LYS e 287 " (cutoff:3.500A) Processing helix chain 'e' and resid 310 through 322 removed outlier: 3.604A pdb=" N GLN e 315 " --> pdb=" O ARG e 311 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU e 316 " --> pdb=" O ASP e 312 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU e 317 " --> pdb=" O SER e 313 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN e 322 " --> pdb=" O LYS e 318 " (cutoff:3.500A) Processing helix chain 'e' and resid 329 through 334 removed outlier: 3.926A pdb=" N VAL e 333 " --> pdb=" O ILE e 329 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN e 334 " --> pdb=" O TRP e 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 329 through 334' Processing helix chain 'e' and resid 433 through 449 Processing helix chain 'e' and resid 509 through 516 Processing helix chain 'e' and resid 522 through 527 Processing helix chain 'f' and resid 16 through 27 removed outlier: 3.719A pdb=" N LYS f 20 " --> pdb=" O SER f 16 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL f 21 " --> pdb=" O GLU f 17 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL f 22 " --> pdb=" O SER f 18 " (cutoff:3.500A) Processing helix chain 'f' and resid 32 through 61 removed outlier: 3.535A pdb=" N ASP f 41 " --> pdb=" O GLN f 37 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU f 42 " --> pdb=" O LEU f 38 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR f 45 " --> pdb=" O ASP f 41 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS f 48 " --> pdb=" O SER f 44 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP f 53 " --> pdb=" O GLU f 49 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS f 56 " --> pdb=" O GLN f 52 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE f 57 " --> pdb=" O ASP f 53 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 76 removed outlier: 4.017A pdb=" N ILE f 71 " --> pdb=" O THR f 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 114 through 119 Processing helix chain 'i' and resid 18 through 26 Processing helix chain 'i' and resid 33 through 61 removed outlier: 4.306A pdb=" N ASN i 37 " --> pdb=" O PRO i 33 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU i 41 " --> pdb=" O ASN i 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA i 43 " --> pdb=" O MET i 39 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP i 52 " --> pdb=" O THR i 48 " (cutoff:3.500A) Processing helix chain 'i' and resid 67 through 77 removed outlier: 3.511A pdb=" N VAL i 71 " --> pdb=" O ASP i 67 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 100 removed outlier: 3.967A pdb=" N ASP i 94 " --> pdb=" O ASP i 90 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN i 98 " --> pdb=" O ASP i 94 " (cutoff:3.500A) Processing helix chain 'j' and resid 115 through 124 Processing helix chain 'j' and resid 131 through 139 Processing helix chain 'j' and resid 148 through 177 removed outlier: 3.939A pdb=" N ILE j 152 " --> pdb=" O ASP j 148 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG j 153 " --> pdb=" O PRO j 149 " (cutoff:3.500A) Processing helix chain 'j' and resid 196 through 205 Proline residue: j 202 - end of helix removed outlier: 3.571A pdb=" N SER j 205 " --> pdb=" O THR j 201 " (cutoff:3.500A) Processing helix chain 'k' and resid 116 through 127 removed outlier: 3.503A pdb=" N ARG k 125 " --> pdb=" O TYR k 121 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER k 127 " --> pdb=" O MET k 123 " (cutoff:3.500A) Processing helix chain 'k' and resid 130 through 143 removed outlier: 4.102A pdb=" N ARG k 136 " --> pdb=" O ALA k 132 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE k 141 " --> pdb=" O LEU k 137 " (cutoff:3.500A) Processing helix chain 'k' and resid 147 through 176 removed outlier: 3.608A pdb=" N ALA k 153 " --> pdb=" O ASN k 149 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER k 158 " --> pdb=" O MET k 154 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS k 159 " --> pdb=" O SER k 155 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU k 167 " --> pdb=" O GLY k 163 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU k 168 " --> pdb=" O GLU k 164 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP k 171 " --> pdb=" O GLU k 167 " (cutoff:3.500A) Processing helix chain 'k' and resid 184 through 197 removed outlier: 3.609A pdb=" N LYS k 197 " --> pdb=" O ARG k 193 " (cutoff:3.500A) Processing helix chain 'l' and resid 61 through 69 Processing helix chain 'l' and resid 77 through 106 Processing helix chain 'l' and resid 113 through 123 removed outlier: 3.743A pdb=" N LEU l 118 " --> pdb=" O LYS l 114 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS l 119 " --> pdb=" O ASP l 115 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU l 120 " --> pdb=" O VAL l 116 " (cutoff:3.500A) Processing helix chain 'l' and resid 145 through 161 removed outlier: 3.794A pdb=" N ALA l 153 " --> pdb=" O LYS l 149 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU l 154 " --> pdb=" O GLN l 150 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE l 155 " --> pdb=" O ARG l 151 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG l 156 " --> pdb=" O MET l 152 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS l 157 " --> pdb=" O ALA l 153 " (cutoff:3.500A) Processing helix chain 'm' and resid 34 through 43 removed outlier: 3.733A pdb=" N CYS m 38 " --> pdb=" O LYS m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 75 Processing helix chain 'm' and resid 82 through 91 Processing helix chain 'm' and resid 93 through 114 Processing sheet with id=AA1, first strand: chain 'P' and resid 190 through 193 removed outlier: 4.404A pdb=" N ASN P 193 " --> pdb=" O ALA P 199 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA P 199 " --> pdb=" O ASN P 193 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR P 209 " --> pdb=" O ILE P 204 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY P 223 " --> pdb=" O ILE P 168 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE P 168 " --> pdb=" O GLY P 223 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU P 165 " --> pdb=" O SER P 261 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N SER P 261 " --> pdb=" O LEU P 165 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR P 171 " --> pdb=" O ILE P 255 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ILE P 255 " --> pdb=" O THR P 171 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASN P 173 " --> pdb=" O PHE P 253 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE P 253 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET P 258 " --> pdb=" O GLY P 314 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY P 314 " --> pdb=" O MET P 258 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE P 300 " --> pdb=" O MET P 295 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'f' and resid 111 through 113 removed outlier: 8.243A pdb=" N SER c 25 " --> pdb=" O LEU j 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 893 through 894 removed outlier: 7.792A pdb=" N GLU d 893 " --> pdb=" O LEU l 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'd' and resid 934 through 936 Processing sheet with id=AA5, first strand: chain 'e' and resid 461 through 466 removed outlier: 6.411A pdb=" N ILE e 461 " --> pdb=" O LEU f 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'e' and resid 473 through 478 removed outlier: 3.851A pdb=" N THR e 493 " --> pdb=" O PHE e 489 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'e' and resid 506 through 507 removed outlier: 4.284A pdb=" N SER e 506 " --> pdb=" O ASP e 529 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'e' and resid 546 through 550 removed outlier: 6.693A pdb=" N SER e 561 " --> pdb=" O TYR e 547 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA e 549 " --> pdb=" O LEU e 559 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU e 559 " --> pdb=" O ALA e 549 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL e 579 " --> pdb=" O LEU e 569 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 588 through 593 Processing sheet with id=AB1, first strand: chain 'e' and resid 632 through 635 removed outlier: 3.635A pdb=" N ARG e 652 " --> pdb=" O THR e 644 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG e 663 " --> pdb=" O LEU e 653 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP e 655 " --> pdb=" O CYS e 661 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS e 661 " --> pdb=" O ASP e 655 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'e' and resid 672 through 677 removed outlier: 6.677A pdb=" N GLY e 687 " --> pdb=" O HIS e 673 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU e 675 " --> pdb=" O ALA e 685 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA e 685 " --> pdb=" O LEU e 675 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE e 677 " --> pdb=" O PHE e 683 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE e 683 " --> pdb=" O PHE e 677 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP e 697 " --> pdb=" O MET e 703 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N MET e 703 " --> pdb=" O ASP e 697 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'e' and resid 716 through 719 removed outlier: 3.779A pdb=" N GLY e 771 " --> pdb=" O LEU e 737 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'e' and resid 782 through 785 removed outlier: 4.239A pdb=" N HIS e 782 " --> pdb=" O ALA e 794 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA e 794 " --> pdb=" O HIS e 782 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 95 through 97 removed outlier: 3.505A pdb=" N LEU f 104 " --> pdb=" O ALA f 97 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2623 1.33 - 1.45: 3131 1.45 - 1.57: 7708 1.57 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 13572 Sorted by residual: bond pdb=" C LYS e 445 " pdb=" O LYS e 445 " ideal model delta sigma weight residual 1.237 1.304 -0.067 1.17e-02 7.31e+03 3.28e+01 bond pdb=" N LEU e 285 " pdb=" CA LEU e 285 " ideal model delta sigma weight residual 1.457 1.515 -0.058 1.29e-02 6.01e+03 2.03e+01 bond pdb=" C HIS j 173 " pdb=" O HIS j 173 " ideal model delta sigma weight residual 1.237 1.287 -0.051 1.17e-02 7.31e+03 1.88e+01 bond pdb=" C ASP e 522 " pdb=" O ASP e 522 " ideal model delta sigma weight residual 1.235 1.289 -0.054 1.26e-02 6.30e+03 1.81e+01 bond pdb=" C HIS m 70 " pdb=" O HIS m 70 " ideal model delta sigma weight residual 1.236 1.285 -0.048 1.15e-02 7.56e+03 1.75e+01 ... (remaining 13567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 17544 2.47 - 4.95: 722 4.95 - 7.42: 48 7.42 - 9.90: 8 9.90 - 12.37: 2 Bond angle restraints: 18324 Sorted by residual: angle pdb=" O PRO f 149 " pdb=" C PRO f 149 " pdb=" N PRO f 150 " ideal model delta sigma weight residual 121.31 125.51 -4.20 4.60e-01 4.73e+00 8.33e+01 angle pdb=" N PRO k 180 " pdb=" CA PRO k 180 " pdb=" C PRO k 180 " ideal model delta sigma weight residual 110.70 119.01 -8.31 1.22e+00 6.72e-01 4.64e+01 angle pdb=" N PRO P 207 " pdb=" CA PRO P 207 " pdb=" C PRO P 207 " ideal model delta sigma weight residual 112.47 100.10 12.37 2.06e+00 2.36e-01 3.61e+01 angle pdb=" N PRO f 150 " pdb=" CA PRO f 150 " pdb=" C PRO f 150 " ideal model delta sigma weight residual 110.70 117.46 -6.76 1.22e+00 6.72e-01 3.07e+01 angle pdb=" C LYS m 71 " pdb=" CA LYS m 71 " pdb=" CB LYS m 71 " ideal model delta sigma weight residual 110.79 119.79 -9.00 1.66e+00 3.63e-01 2.94e+01 ... (remaining 18319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 7386 17.74 - 35.48: 738 35.48 - 53.22: 145 53.22 - 70.96: 32 70.96 - 88.70: 11 Dihedral angle restraints: 8312 sinusoidal: 3466 harmonic: 4846 Sorted by residual: dihedral pdb=" C LYS m 71 " pdb=" N LYS m 71 " pdb=" CA LYS m 71 " pdb=" CB LYS m 71 " ideal model delta harmonic sigma weight residual -122.60 -137.43 14.83 0 2.50e+00 1.60e-01 3.52e+01 dihedral pdb=" C PHE e 267 " pdb=" N PHE e 267 " pdb=" CA PHE e 267 " pdb=" CB PHE e 267 " ideal model delta harmonic sigma weight residual -122.60 -135.42 12.82 0 2.50e+00 1.60e-01 2.63e+01 dihedral pdb=" N LYS m 71 " pdb=" C LYS m 71 " pdb=" CA LYS m 71 " pdb=" CB LYS m 71 " ideal model delta harmonic sigma weight residual 122.80 134.76 -11.96 0 2.50e+00 1.60e-01 2.29e+01 ... (remaining 8309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1670 0.099 - 0.197: 305 0.197 - 0.296: 48 0.296 - 0.395: 4 0.395 - 0.493: 3 Chirality restraints: 2030 Sorted by residual: chirality pdb=" CB ILE f 92 " pdb=" CA ILE f 92 " pdb=" CG1 ILE f 92 " pdb=" CG2 ILE f 92 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.08e+00 chirality pdb=" CA LYS m 71 " pdb=" N LYS m 71 " pdb=" C LYS m 71 " pdb=" CB LYS m 71 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" CA PHE e 267 " pdb=" N PHE e 267 " pdb=" C PHE e 267 " pdb=" CB PHE e 267 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 2027 not shown) Planarity restraints: 2364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU e 285 " 0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C LEU e 285 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU e 285 " 0.029 2.00e-02 2.50e+03 pdb=" N THR e 286 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS e 449 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C LYS e 449 " -0.069 2.00e-02 2.50e+03 pdb=" O LYS e 449 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG e 450 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS e 508 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.48e+01 pdb=" C LYS e 508 " -0.066 2.00e-02 2.50e+03 pdb=" O LYS e 508 " 0.025 2.00e-02 2.50e+03 pdb=" N GLN e 509 " 0.022 2.00e-02 2.50e+03 ... (remaining 2361 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1251 2.75 - 3.29: 12527 3.29 - 3.82: 20864 3.82 - 4.36: 26765 4.36 - 4.90: 44560 Nonbonded interactions: 105967 Sorted by model distance: nonbonded pdb=" OG SER e 562 " pdb=" OD1 ASP e 564 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR d1080 " pdb=" OD2 ASP e 606 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR e 474 " pdb=" O VAL e 546 " model vdw 2.277 3.040 nonbonded pdb=" O LEU j 123 " pdb=" N ASP j 125 " model vdw 2.302 3.120 nonbonded pdb=" N ASP e 277 " pdb=" OD1 ASP e 277 " model vdw 2.321 3.120 ... (remaining 105962 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.580 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 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 : 0.008 0.067 13572 Z= 0.519 Angle : 1.065 12.371 18324 Z= 0.735 Chirality : 0.079 0.493 2030 Planarity : 0.008 0.069 2364 Dihedral : 14.832 88.705 5166 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.41 % Favored : 93.34 % Rotamer: Outliers : 2.11 % Allowed : 7.83 % Favored : 90.06 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.20), residues: 1622 helix: -1.32 (0.20), residues: 718 sheet: -2.37 (0.33), residues: 200 loop : -2.56 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG e 682 TYR 0.027 0.002 TYR j 216 PHE 0.025 0.002 PHE e 600 TRP 0.020 0.002 TRP e 612 HIS 0.007 0.001 HIS e 584 Details of bonding type rmsd covalent geometry : bond 0.00774 (13572) covalent geometry : angle 1.06515 (18324) hydrogen bonds : bond 0.24232 ( 550) hydrogen bonds : angle 8.79011 ( 1617) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 421 time to evaluate : 0.549 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 36 ASP cc_start: 0.7979 (t0) cc_final: 0.7375 (t0) REVERT: c 89 PRO cc_start: 0.8081 (Cg_exo) cc_final: 0.7559 (Cg_endo) REVERT: e 270 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6891 (t0) REVERT: e 282 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7439 (mt) REVERT: f 58 MET cc_start: 0.7737 (ttp) cc_final: 0.7186 (ttt) outliers start: 31 outliers final: 9 residues processed: 438 average time/residue: 0.1653 time to fit residues: 95.5892 Evaluate side-chains 360 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 349 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 24 ASP Chi-restraints excluded: chain e residue 268 HIS Chi-restraints excluded: chain e residue 270 ASP Chi-restraints excluded: chain e residue 277 ASP Chi-restraints excluded: chain e residue 282 LEU Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 579 VAL Chi-restraints excluded: chain m residue 55 ASP Chi-restraints excluded: chain m residue 58 GLU Chi-restraints excluded: chain m residue 77 ARG Chi-restraints excluded: chain m residue 84 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 189 ASN P 193 ASN P 327 ASN c 16 GLN c 19 GLN c 44 GLN c 85 HIS d 912 ASN d1069 ASN e 256 HIS e 425 ASN e 673 HIS e 784 HIS i 81 GLN j 160 GLN j 173 HIS k 139 GLN k 186 HIS l 73 ASN l 101 GLN l 148 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.156952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.100915 restraints weight = 18083.981| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.89 r_work: 0.3112 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13572 Z= 0.170 Angle : 0.691 12.201 18324 Z= 0.353 Chirality : 0.045 0.258 2030 Planarity : 0.006 0.058 2364 Dihedral : 5.969 49.537 1830 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.31 % Allowed : 15.86 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.20), residues: 1622 helix: -0.28 (0.19), residues: 715 sheet: -1.83 (0.36), residues: 185 loop : -2.20 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG e 280 TYR 0.021 0.002 TYR j 216 PHE 0.019 0.002 PHE e 264 TRP 0.024 0.002 TRP e 612 HIS 0.006 0.001 HIS l 119 Details of bonding type rmsd covalent geometry : bond 0.00390 (13572) covalent geometry : angle 0.69140 (18324) hydrogen bonds : bond 0.05402 ( 550) hydrogen bonds : angle 4.89740 ( 1617) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 368 time to evaluate : 0.516 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 202 MET cc_start: 0.4818 (ttt) cc_final: 0.4469 (tpp) REVERT: c 81 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7934 (mm-30) REVERT: c 84 ILE cc_start: 0.8271 (tt) cc_final: 0.8034 (tt) REVERT: c 105 ASN cc_start: 0.8743 (m-40) cc_final: 0.8496 (m110) REVERT: d 851 ARG cc_start: 0.8365 (mtp-110) cc_final: 0.8120 (ptm160) REVERT: d 958 LYS cc_start: 0.9421 (tppt) cc_final: 0.9130 (tppt) REVERT: e 265 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8133 (tp30) REVERT: e 328 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8339 (tt0) REVERT: e 444 MET cc_start: 0.8000 (tmm) cc_final: 0.7791 (tmm) REVERT: e 526 ARG cc_start: 0.8407 (tpp80) cc_final: 0.7898 (tpp80) REVERT: f 17 GLU cc_start: 0.8428 (mp0) cc_final: 0.8148 (mp0) REVERT: f 87 HIS cc_start: 0.8882 (m-70) cc_final: 0.8673 (m-70) REVERT: i 97 ARG cc_start: 0.8670 (ttp-170) cc_final: 0.8208 (ttp80) REVERT: i 110 TYR cc_start: 0.8772 (m-80) cc_final: 0.8011 (m-10) REVERT: j 118 ASP cc_start: 0.9063 (m-30) cc_final: 0.8782 (m-30) REVERT: j 122 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: j 175 LYS cc_start: 0.8774 (mttt) cc_final: 0.8398 (mttp) REVERT: k 123 MET cc_start: 0.9104 (mmm) cc_final: 0.8716 (mmt) REVERT: k 144 THR cc_start: 0.7150 (OUTLIER) cc_final: 0.6859 (t) REVERT: k 164 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8559 (mt-10) REVERT: l 56 GLN cc_start: 0.7834 (pt0) cc_final: 0.6912 (mp10) REVERT: l 64 GLN cc_start: 0.8035 (tp40) cc_final: 0.7640 (tp40) REVERT: l 150 GLN cc_start: 0.8867 (tt0) cc_final: 0.8658 (tt0) REVERT: m 80 ARG cc_start: 0.7758 (mmm-85) cc_final: 0.7413 (mmm-85) REVERT: m 102 ASP cc_start: 0.8184 (m-30) cc_final: 0.7875 (t0) outliers start: 34 outliers final: 20 residues processed: 383 average time/residue: 0.1580 time to fit residues: 80.3662 Evaluate side-chains 368 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 346 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 280 PHE Chi-restraints excluded: chain e residue 268 HIS Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 712 ASP Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain j residue 122 GLN Chi-restraints excluded: chain k residue 140 SER Chi-restraints excluded: chain k residue 144 THR Chi-restraints excluded: chain k residue 145 SER Chi-restraints excluded: chain k residue 155 SER Chi-restraints excluded: chain k residue 173 CYS Chi-restraints excluded: chain l residue 101 GLN Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain m residue 81 VAL Chi-restraints excluded: chain m residue 84 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 77 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 327 ASN c 104 ASN ** e 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 638 ASN j 122 GLN k 139 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.150736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097375 restraints weight = 18771.664| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.29 r_work: 0.3005 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 13572 Z= 0.324 Angle : 0.766 11.968 18324 Z= 0.386 Chirality : 0.049 0.204 2030 Planarity : 0.006 0.057 2364 Dihedral : 5.496 48.842 1812 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.61 % Allowed : 17.90 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.20), residues: 1622 helix: 0.20 (0.19), residues: 716 sheet: -1.78 (0.35), residues: 195 loop : -1.93 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG f 124 TYR 0.019 0.002 TYR j 138 PHE 0.016 0.002 PHE m 64 TRP 0.023 0.002 TRP e 612 HIS 0.009 0.001 HIS e 256 Details of bonding type rmsd covalent geometry : bond 0.00771 (13572) covalent geometry : angle 0.76557 (18324) hydrogen bonds : bond 0.05332 ( 550) hydrogen bonds : angle 4.69647 ( 1617) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 354 time to evaluate : 0.523 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: P 202 MET cc_start: 0.5224 (ttt) cc_final: 0.4944 (tpp) REVERT: P 219 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6381 (tmm) REVERT: P 231 ARG cc_start: 0.9322 (ptp-110) cc_final: 0.8923 (ptt-90) REVERT: P 283 TYR cc_start: 0.8410 (t80) cc_final: 0.8095 (t80) REVERT: P 299 ARG cc_start: 0.9687 (mmm-85) cc_final: 0.9367 (mmp80) REVERT: P 312 LEU cc_start: 0.8118 (mp) cc_final: 0.7879 (pp) REVERT: c 36 ASP cc_start: 0.8885 (t0) cc_final: 0.8335 (t0) REVERT: c 89 PRO cc_start: 0.9093 (Cg_exo) cc_final: 0.8777 (Cg_endo) REVERT: c 105 ASN cc_start: 0.8652 (m-40) cc_final: 0.8171 (m110) REVERT: d 851 ARG cc_start: 0.8423 (mtp-110) cc_final: 0.8195 (ptm160) REVERT: d 924 LYS cc_start: 0.8411 (mttt) cc_final: 0.8079 (mttt) REVERT: d 931 ASP cc_start: 0.8214 (t0) cc_final: 0.7927 (t0) REVERT: d 958 LYS cc_start: 0.9433 (tppt) cc_final: 0.9135 (tppt) REVERT: e 216 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7616 (pt0) REVERT: e 235 GLU cc_start: 0.9074 (tt0) cc_final: 0.8829 (tt0) REVERT: e 268 HIS cc_start: 0.8447 (p90) cc_final: 0.8171 (p90) REVERT: e 444 MET cc_start: 0.8019 (tmm) cc_final: 0.7748 (tmm) REVERT: e 774 MET cc_start: 0.8726 (mmm) cc_final: 0.8416 (mmm) REVERT: f 17 GLU cc_start: 0.8478 (mp0) cc_final: 0.8171 (mp0) REVERT: i 62 LYS cc_start: 0.9203 (mtmm) cc_final: 0.8975 (mtpp) REVERT: i 76 GLN cc_start: 0.8768 (tt0) cc_final: 0.8489 (tt0) REVERT: i 97 ARG cc_start: 0.8709 (ttp-110) cc_final: 0.8456 (ttp80) REVERT: i 119 ARG cc_start: 0.8902 (ptt-90) cc_final: 0.8430 (ptt180) REVERT: i 120 TYR cc_start: 0.9151 (m-80) cc_final: 0.8683 (m-80) REVERT: j 118 ASP cc_start: 0.9096 (m-30) cc_final: 0.8803 (m-30) REVERT: k 139 GLN cc_start: 0.8808 (mt0) cc_final: 0.8432 (mm-40) REVERT: k 164 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8613 (mt-10) REVERT: k 167 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8240 (tp30) REVERT: k 168 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8322 (tm-30) REVERT: l 60 LYS cc_start: 0.9150 (tttt) cc_final: 0.7016 (ttmm) REVERT: l 64 GLN cc_start: 0.8088 (tp40) cc_final: 0.7870 (tp40) REVERT: l 78 GLU cc_start: 0.8080 (mp0) cc_final: 0.7693 (tp30) REVERT: l 81 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7720 (pt0) REVERT: m 30 ARG cc_start: 0.8558 (mmt180) cc_final: 0.8083 (mmm-85) REVERT: m 90 ILE cc_start: 0.8701 (tp) cc_final: 0.8489 (tp) outliers start: 53 outliers final: 33 residues processed: 377 average time/residue: 0.1692 time to fit residues: 84.3005 Evaluate side-chains 373 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 338 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 254 LYS Chi-restraints excluded: chain P residue 280 PHE Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain d residue 860 VAL Chi-restraints excluded: chain d residue 929 LYS Chi-restraints excluded: chain d residue 1059 ASN Chi-restraints excluded: chain d residue 1078 LEU Chi-restraints excluded: chain d residue 1081 LYS Chi-restraints excluded: chain e residue 216 GLU Chi-restraints excluded: chain e residue 277 ASP Chi-restraints excluded: chain e residue 298 LEU Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 675 LEU Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain k residue 140 SER Chi-restraints excluded: chain k residue 144 THR Chi-restraints excluded: chain k residue 145 SER Chi-restraints excluded: chain k residue 173 CYS Chi-restraints excluded: chain l residue 109 SER Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain m residue 81 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 104 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 117 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 33 optimal weight: 0.0040 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 256 GLN ** e 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 76 GLN j 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.154526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.098746 restraints weight = 18252.839| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.92 r_work: 0.3080 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13572 Z= 0.144 Angle : 0.643 13.999 18324 Z= 0.320 Chirality : 0.044 0.203 2030 Planarity : 0.005 0.046 2364 Dihedral : 4.810 29.005 1807 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.54 % Allowed : 18.99 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.21), residues: 1622 helix: 0.71 (0.20), residues: 725 sheet: -1.41 (0.36), residues: 190 loop : -1.76 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG f 124 TYR 0.023 0.002 TYR e 275 PHE 0.016 0.001 PHE e 600 TRP 0.018 0.002 TRP e 612 HIS 0.006 0.001 HIS e 256 Details of bonding type rmsd covalent geometry : bond 0.00333 (13572) covalent geometry : angle 0.64335 (18324) hydrogen bonds : bond 0.04078 ( 550) hydrogen bonds : angle 4.29415 ( 1617) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 343 time to evaluate : 0.493 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: P 202 MET cc_start: 0.5176 (ttt) cc_final: 0.4913 (tpp) REVERT: P 219 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.6469 (tmm) REVERT: P 269 ARG cc_start: 0.7705 (mtm110) cc_final: 0.7475 (mtm110) REVERT: P 271 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8073 (mm-30) REVERT: P 299 ARG cc_start: 0.9667 (mmm-85) cc_final: 0.9367 (mmp80) REVERT: P 312 LEU cc_start: 0.8079 (mp) cc_final: 0.7879 (pp) REVERT: P 316 LYS cc_start: 0.9614 (mmmm) cc_final: 0.9357 (mmmt) REVERT: c 19 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7320 (tp40) REVERT: c 105 ASN cc_start: 0.8717 (m-40) cc_final: 0.8341 (m110) REVERT: d 924 LYS cc_start: 0.8500 (mttt) cc_final: 0.8287 (mttt) REVERT: d 928 TYR cc_start: 0.9076 (m-80) cc_final: 0.8679 (m-80) REVERT: d 931 ASP cc_start: 0.8162 (t0) cc_final: 0.7802 (t0) REVERT: e 210 ASP cc_start: 0.8472 (m-30) cc_final: 0.7557 (t0) REVERT: e 216 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7452 (pt0) REVERT: e 235 GLU cc_start: 0.9084 (tt0) cc_final: 0.8756 (tt0) REVERT: e 425 ASN cc_start: 0.9164 (t0) cc_final: 0.8775 (t0) REVERT: e 444 MET cc_start: 0.7989 (tmm) cc_final: 0.7724 (tmm) REVERT: e 526 ARG cc_start: 0.8331 (tpp80) cc_final: 0.7942 (tpp80) REVERT: e 774 MET cc_start: 0.8758 (mmm) cc_final: 0.8432 (mmm) REVERT: f 17 GLU cc_start: 0.8390 (mp0) cc_final: 0.8105 (mp0) REVERT: f 65 LYS cc_start: 0.7879 (tptt) cc_final: 0.7300 (tppt) REVERT: i 62 LYS cc_start: 0.9151 (mtmm) cc_final: 0.8950 (mtpp) REVERT: i 97 ARG cc_start: 0.8505 (ttp-110) cc_final: 0.8284 (ttm110) REVERT: i 114 ARG cc_start: 0.8688 (mtt90) cc_final: 0.8462 (mtt-85) REVERT: i 119 ARG cc_start: 0.8831 (ptt-90) cc_final: 0.8345 (ptt180) REVERT: i 120 TYR cc_start: 0.9134 (m-80) cc_final: 0.8623 (m-80) REVERT: j 118 ASP cc_start: 0.9054 (m-30) cc_final: 0.8761 (m-30) REVERT: j 175 LYS cc_start: 0.8747 (mttt) cc_final: 0.8422 (mttm) REVERT: k 122 GLU cc_start: 0.8863 (tt0) cc_final: 0.8339 (tp30) REVERT: k 123 MET cc_start: 0.9152 (mmm) cc_final: 0.8873 (mmm) REVERT: k 139 GLN cc_start: 0.8796 (mt0) cc_final: 0.8446 (mm-40) REVERT: k 167 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8188 (tp30) REVERT: k 168 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8056 (tm-30) REVERT: l 60 LYS cc_start: 0.9119 (tttt) cc_final: 0.6898 (ttmm) REVERT: l 78 GLU cc_start: 0.7915 (mp0) cc_final: 0.7506 (tp30) REVERT: l 81 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7622 (pt0) REVERT: m 90 ILE cc_start: 0.8638 (tp) cc_final: 0.8400 (tp) outliers start: 52 outliers final: 35 residues processed: 363 average time/residue: 0.1588 time to fit residues: 76.4952 Evaluate side-chains 369 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 331 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 225 LYS Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 254 LYS Chi-restraints excluded: chain P residue 280 PHE Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain c residue 19 GLN Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain d residue 885 ILE Chi-restraints excluded: chain d residue 1059 ASN Chi-restraints excluded: chain d residue 1081 LYS Chi-restraints excluded: chain e residue 216 GLU Chi-restraints excluded: chain e residue 268 HIS Chi-restraints excluded: chain e residue 298 LEU Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 563 GLU Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 674 SER Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 712 ASP Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain j residue 194 THR Chi-restraints excluded: chain k residue 144 THR Chi-restraints excluded: chain k residue 173 CYS Chi-restraints excluded: chain l residue 101 GLN Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain m residue 81 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 47 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 76 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.153982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098009 restraints weight = 18494.814| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.92 r_work: 0.3068 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13572 Z= 0.167 Angle : 0.637 13.397 18324 Z= 0.317 Chirality : 0.044 0.232 2030 Planarity : 0.005 0.067 2364 Dihedral : 4.735 29.276 1807 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.95 % Allowed : 19.67 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.21), residues: 1622 helix: 0.98 (0.20), residues: 726 sheet: -1.38 (0.37), residues: 192 loop : -1.69 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG f 124 TYR 0.026 0.002 TYR e 275 PHE 0.025 0.001 PHE e 267 TRP 0.020 0.001 TRP e 612 HIS 0.007 0.001 HIS e 256 Details of bonding type rmsd covalent geometry : bond 0.00395 (13572) covalent geometry : angle 0.63671 (18324) hydrogen bonds : bond 0.04080 ( 550) hydrogen bonds : angle 4.20465 ( 1617) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 346 time to evaluate : 0.511 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: P 219 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.6511 (tmm) REVERT: P 231 ARG cc_start: 0.9278 (ptp-110) cc_final: 0.9018 (ptp90) REVERT: P 299 ARG cc_start: 0.9677 (mmm-85) cc_final: 0.9408 (mmp80) REVERT: P 312 LEU cc_start: 0.8119 (mp) cc_final: 0.7866 (pp) REVERT: c 1 MET cc_start: 0.5940 (tpt) cc_final: 0.4978 (tpp) REVERT: c 19 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.7314 (tp40) REVERT: c 105 ASN cc_start: 0.8778 (m-40) cc_final: 0.8417 (m110) REVERT: d 931 ASP cc_start: 0.8217 (t0) cc_final: 0.7830 (t0) REVERT: d 958 LYS cc_start: 0.9395 (tppt) cc_final: 0.8924 (ttmm) REVERT: e 216 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7644 (pt0) REVERT: e 235 GLU cc_start: 0.9074 (tt0) cc_final: 0.8736 (tt0) REVERT: e 280 ARG cc_start: 0.8873 (ttp80) cc_final: 0.8652 (tmm160) REVERT: e 444 MET cc_start: 0.8008 (tmm) cc_final: 0.7766 (tmm) REVERT: e 526 ARG cc_start: 0.8308 (tpp80) cc_final: 0.7959 (tpp80) REVERT: e 774 MET cc_start: 0.8755 (mmm) cc_final: 0.8406 (mmm) REVERT: f 17 GLU cc_start: 0.8357 (mp0) cc_final: 0.8054 (mp0) REVERT: f 65 LYS cc_start: 0.7889 (tptt) cc_final: 0.7361 (tppt) REVERT: i 14 LYS cc_start: 0.8445 (tttm) cc_final: 0.8117 (tppt) REVERT: i 21 GLN cc_start: 0.8304 (tp-100) cc_final: 0.7706 (tp40) REVERT: i 78 ARG cc_start: 0.5506 (OUTLIER) cc_final: 0.4956 (mmt90) REVERT: i 97 ARG cc_start: 0.8417 (ttp-110) cc_final: 0.8135 (ttp80) REVERT: i 114 ARG cc_start: 0.8671 (mtt90) cc_final: 0.8447 (mtt-85) REVERT: j 118 ASP cc_start: 0.9090 (m-30) cc_final: 0.8865 (m-30) REVERT: j 124 GLU cc_start: 0.9077 (tp30) cc_final: 0.8667 (tp30) REVERT: j 165 ASP cc_start: 0.8048 (m-30) cc_final: 0.7812 (m-30) REVERT: j 175 LYS cc_start: 0.8668 (mttt) cc_final: 0.8358 (mttm) REVERT: k 139 GLN cc_start: 0.8750 (mt0) cc_final: 0.8477 (mm-40) REVERT: k 167 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8215 (tp30) REVERT: k 193 ARG cc_start: 0.8624 (ttm-80) cc_final: 0.8334 (ttm-80) REVERT: l 60 LYS cc_start: 0.9119 (tttt) cc_final: 0.6811 (ttmm) REVERT: l 78 GLU cc_start: 0.7952 (mp0) cc_final: 0.7460 (tp30) REVERT: l 81 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7562 (pt0) REVERT: l 150 GLN cc_start: 0.8901 (tt0) cc_final: 0.8364 (tt0) REVERT: m 104 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8053 (mm) outliers start: 58 outliers final: 43 residues processed: 367 average time/residue: 0.1679 time to fit residues: 81.4120 Evaluate side-chains 385 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 337 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 225 LYS Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 254 LYS Chi-restraints excluded: chain P residue 280 PHE Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain c residue 19 GLN Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain d residue 885 ILE Chi-restraints excluded: chain d residue 1059 ASN Chi-restraints excluded: chain d residue 1078 LEU Chi-restraints excluded: chain d residue 1081 LYS Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 216 GLU Chi-restraints excluded: chain e residue 268 HIS Chi-restraints excluded: chain e residue 298 LEU Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 479 THR Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 563 GLU Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 674 SER Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 712 ASP Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 44 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 194 THR Chi-restraints excluded: chain k residue 140 SER Chi-restraints excluded: chain k residue 145 SER Chi-restraints excluded: chain k residue 173 CYS Chi-restraints excluded: chain l residue 101 GLN Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain m residue 81 VAL Chi-restraints excluded: chain m residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 42 optimal weight: 0.9990 chunk 113 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 33 optimal weight: 0.0370 chunk 91 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 936 GLN ** e 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.155176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.099497 restraints weight = 18289.285| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.90 r_work: 0.3095 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13572 Z= 0.134 Angle : 0.634 14.617 18324 Z= 0.313 Chirality : 0.043 0.222 2030 Planarity : 0.004 0.044 2364 Dihedral : 4.590 28.822 1807 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.61 % Allowed : 21.24 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.21), residues: 1622 helix: 1.13 (0.20), residues: 733 sheet: -1.24 (0.36), residues: 197 loop : -1.65 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG f 124 TYR 0.023 0.001 TYR e 275 PHE 0.037 0.001 PHE e 267 TRP 0.018 0.001 TRP e 612 HIS 0.003 0.001 HIS e 256 Details of bonding type rmsd covalent geometry : bond 0.00318 (13572) covalent geometry : angle 0.63381 (18324) hydrogen bonds : bond 0.03729 ( 550) hydrogen bonds : angle 4.08562 ( 1617) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 348 time to evaluate : 0.512 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: symmetry clash revert: symmetry clash REVERT: P 219 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.6558 (tmm) REVERT: P 231 ARG cc_start: 0.9218 (ptp-110) cc_final: 0.8868 (ptp-170) REVERT: P 269 ARG cc_start: 0.7694 (mtm110) cc_final: 0.7308 (mpp80) REVERT: P 299 ARG cc_start: 0.9646 (mmm-85) cc_final: 0.9430 (mmp80) REVERT: P 312 LEU cc_start: 0.8098 (mp) cc_final: 0.7857 (pp) REVERT: c 1 MET cc_start: 0.5951 (tpt) cc_final: 0.4989 (tpp) REVERT: c 19 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7273 (tp40) REVERT: c 105 ASN cc_start: 0.8774 (m-40) cc_final: 0.8435 (m110) REVERT: d 851 ARG cc_start: 0.8092 (ptm160) cc_final: 0.7868 (ptm-80) REVERT: d 915 GLU cc_start: 0.8167 (pt0) cc_final: 0.7957 (pt0) REVERT: d 924 LYS cc_start: 0.8254 (mttt) cc_final: 0.8005 (mttt) REVERT: d 928 TYR cc_start: 0.9067 (m-80) cc_final: 0.8587 (m-80) REVERT: d 931 ASP cc_start: 0.8288 (t0) cc_final: 0.7894 (t0) REVERT: e 213 MET cc_start: 0.7239 (mmm) cc_final: 0.6779 (mmm) REVERT: e 216 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7592 (pt0) REVERT: e 235 GLU cc_start: 0.9099 (tt0) cc_final: 0.8767 (tt0) REVERT: e 444 MET cc_start: 0.7982 (tmm) cc_final: 0.7724 (tmm) REVERT: e 526 ARG cc_start: 0.8311 (tpp80) cc_final: 0.7954 (tpp80) REVERT: e 634 ARG cc_start: 0.8755 (mmt-90) cc_final: 0.8497 (tpp-160) REVERT: e 774 MET cc_start: 0.8773 (mmm) cc_final: 0.8421 (mmm) REVERT: f 17 GLU cc_start: 0.8314 (mp0) cc_final: 0.8011 (mp0) REVERT: f 65 LYS cc_start: 0.7840 (tptt) cc_final: 0.7310 (tppt) REVERT: f 103 GLU cc_start: 0.8399 (tt0) cc_final: 0.7875 (mp0) REVERT: i 14 LYS cc_start: 0.8447 (tttm) cc_final: 0.8121 (tppt) REVERT: i 21 GLN cc_start: 0.8292 (tp-100) cc_final: 0.7742 (tp40) REVERT: i 78 ARG cc_start: 0.5467 (OUTLIER) cc_final: 0.4942 (mmt90) REVERT: i 97 ARG cc_start: 0.8391 (ttp-110) cc_final: 0.8036 (ttp80) REVERT: i 114 ARG cc_start: 0.8657 (mtt90) cc_final: 0.8439 (mtt-85) REVERT: j 118 ASP cc_start: 0.9063 (m-30) cc_final: 0.8854 (m-30) REVERT: j 124 GLU cc_start: 0.9070 (tp30) cc_final: 0.8726 (tp30) REVERT: j 175 LYS cc_start: 0.8655 (mttt) cc_final: 0.8347 (mttm) REVERT: k 167 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8202 (tp30) REVERT: k 168 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7972 (tm-30) REVERT: k 193 ARG cc_start: 0.8647 (ttm-80) cc_final: 0.8412 (ttm-80) REVERT: k 199 GLN cc_start: 0.8629 (mm110) cc_final: 0.8386 (mm-40) REVERT: l 60 LYS cc_start: 0.9103 (tttt) cc_final: 0.6899 (ttmm) REVERT: l 78 GLU cc_start: 0.7907 (mp0) cc_final: 0.7431 (tp30) REVERT: l 81 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7596 (pt0) REVERT: l 150 GLN cc_start: 0.8849 (tt0) cc_final: 0.8303 (tt0) REVERT: m 73 MET cc_start: 0.8065 (mtp) cc_final: 0.7862 (mtm) outliers start: 53 outliers final: 40 residues processed: 371 average time/residue: 0.1638 time to fit residues: 80.8216 Evaluate side-chains 380 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 336 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 225 LYS Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain c residue 19 GLN Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain d residue 885 ILE Chi-restraints excluded: chain d residue 1059 ASN Chi-restraints excluded: chain d residue 1078 LEU Chi-restraints excluded: chain d residue 1081 LYS Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 216 GLU Chi-restraints excluded: chain e residue 298 LEU Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 479 THR Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 563 GLU Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 674 SER Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 712 ASP Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 44 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 123 LEU Chi-restraints excluded: chain j residue 215 HIS Chi-restraints excluded: chain k residue 144 THR Chi-restraints excluded: chain k residue 173 CYS Chi-restraints excluded: chain l residue 101 GLN Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain m residue 81 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 145 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 148 optimal weight: 0.0070 chunk 149 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 16 GLN c 71 GLN ** e 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.153833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.098073 restraints weight = 18354.195| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.89 r_work: 0.3073 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13572 Z= 0.176 Angle : 0.658 14.769 18324 Z= 0.325 Chirality : 0.044 0.232 2030 Planarity : 0.004 0.044 2364 Dihedral : 4.580 28.826 1807 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.81 % Allowed : 21.31 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.21), residues: 1622 helix: 1.25 (0.20), residues: 728 sheet: -1.20 (0.36), residues: 197 loop : -1.58 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 318 TYR 0.021 0.001 TYR e 275 PHE 0.038 0.002 PHE e 267 TRP 0.020 0.002 TRP e 612 HIS 0.005 0.001 HIS e 784 Details of bonding type rmsd covalent geometry : bond 0.00428 (13572) covalent geometry : angle 0.65780 (18324) hydrogen bonds : bond 0.03905 ( 550) hydrogen bonds : angle 4.10907 ( 1617) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 338 time to evaluate : 0.468 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: symmetry clash revert: symmetry clash REVERT: P 205 ARG cc_start: 0.5427 (mmp80) cc_final: 0.5226 (mmp80) REVERT: P 219 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.6590 (tmm) REVERT: P 269 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7206 (mpp80) REVERT: P 271 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8534 (mm-30) REVERT: P 312 LEU cc_start: 0.8036 (mp) cc_final: 0.7816 (pp) REVERT: c 1 MET cc_start: 0.5920 (tpt) cc_final: 0.4985 (tpp) REVERT: c 19 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.7291 (tp40) REVERT: c 105 ASN cc_start: 0.8786 (m-40) cc_final: 0.8489 (m110) REVERT: d 915 GLU cc_start: 0.8178 (pt0) cc_final: 0.7949 (pt0) REVERT: d 928 TYR cc_start: 0.9083 (m-80) cc_final: 0.8674 (m-80) REVERT: d 929 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8657 (mmmt) REVERT: d 931 ASP cc_start: 0.8276 (t0) cc_final: 0.7863 (t0) REVERT: d 932 ASP cc_start: 0.8851 (t70) cc_final: 0.8589 (t0) REVERT: d 958 LYS cc_start: 0.9373 (tppt) cc_final: 0.8960 (tppp) REVERT: e 213 MET cc_start: 0.7265 (mmm) cc_final: 0.6786 (mmm) REVERT: e 216 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7674 (pt0) REVERT: e 235 GLU cc_start: 0.9102 (tt0) cc_final: 0.8758 (tt0) REVERT: e 280 ARG cc_start: 0.8860 (ttp80) cc_final: 0.8633 (tmm160) REVERT: e 444 MET cc_start: 0.8004 (tmm) cc_final: 0.7734 (tmm) REVERT: e 492 SER cc_start: 0.9156 (OUTLIER) cc_final: 0.8736 (m) REVERT: e 515 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9003 (mm) REVERT: e 526 ARG cc_start: 0.8324 (tpp80) cc_final: 0.7969 (tpp80) REVERT: e 774 MET cc_start: 0.8769 (mmm) cc_final: 0.8399 (mmm) REVERT: f 17 GLU cc_start: 0.8329 (mp0) cc_final: 0.8022 (mp0) REVERT: f 65 LYS cc_start: 0.7842 (tptt) cc_final: 0.7319 (tppt) REVERT: f 103 GLU cc_start: 0.8408 (tt0) cc_final: 0.7891 (mp0) REVERT: i 14 LYS cc_start: 0.8495 (tttm) cc_final: 0.8143 (tppt) REVERT: i 21 GLN cc_start: 0.8306 (tp-100) cc_final: 0.7751 (tp40) REVERT: i 78 ARG cc_start: 0.5412 (OUTLIER) cc_final: 0.4910 (mmt90) REVERT: i 97 ARG cc_start: 0.8403 (ttp-110) cc_final: 0.8021 (ttp80) REVERT: i 114 ARG cc_start: 0.8671 (mtt90) cc_final: 0.8452 (mtt-85) REVERT: j 118 ASP cc_start: 0.9094 (m-30) cc_final: 0.8893 (m-30) REVERT: j 124 GLU cc_start: 0.9102 (tp30) cc_final: 0.8762 (tp30) REVERT: j 165 ASP cc_start: 0.8023 (m-30) cc_final: 0.7784 (m-30) REVERT: j 175 LYS cc_start: 0.8673 (mttt) cc_final: 0.8382 (mttm) REVERT: k 117 GLN cc_start: 0.8315 (pp30) cc_final: 0.7916 (pp30) REVERT: k 167 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8197 (tp30) REVERT: k 193 ARG cc_start: 0.8647 (ttm-80) cc_final: 0.8397 (ttm-80) REVERT: k 199 GLN cc_start: 0.8648 (mm110) cc_final: 0.8419 (mm-40) REVERT: l 150 GLN cc_start: 0.8829 (tt0) cc_final: 0.8275 (tt0) REVERT: m 30 ARG cc_start: 0.8159 (mmt180) cc_final: 0.7867 (mmm-85) outliers start: 56 outliers final: 45 residues processed: 366 average time/residue: 0.1649 time to fit residues: 79.5526 Evaluate side-chains 383 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 331 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 225 LYS Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 19 GLN Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain d residue 885 ILE Chi-restraints excluded: chain d residue 929 LYS Chi-restraints excluded: chain d residue 1059 ASN Chi-restraints excluded: chain d residue 1078 LEU Chi-restraints excluded: chain d residue 1081 LYS Chi-restraints excluded: chain e residue 216 GLU Chi-restraints excluded: chain e residue 298 LEU Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 479 THR Chi-restraints excluded: chain e residue 492 SER Chi-restraints excluded: chain e residue 515 LEU Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 563 GLU Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 674 SER Chi-restraints excluded: chain e residue 675 LEU Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 712 ASP Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 44 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 194 THR Chi-restraints excluded: chain j residue 215 HIS Chi-restraints excluded: chain k residue 141 ILE Chi-restraints excluded: chain k residue 144 THR Chi-restraints excluded: chain k residue 173 CYS Chi-restraints excluded: chain l residue 101 GLN Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain m residue 81 VAL Chi-restraints excluded: chain m residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 110 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 158 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 71 GLN ** e 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.153675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097592 restraints weight = 18210.728| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.91 r_work: 0.3068 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13572 Z= 0.177 Angle : 0.666 15.131 18324 Z= 0.329 Chirality : 0.045 0.321 2030 Planarity : 0.004 0.051 2364 Dihedral : 4.581 28.972 1807 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.81 % Allowed : 21.92 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.21), residues: 1622 helix: 1.30 (0.20), residues: 722 sheet: -1.20 (0.36), residues: 198 loop : -1.54 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG f 124 TYR 0.020 0.001 TYR e 275 PHE 0.029 0.002 PHE e 267 TRP 0.020 0.002 TRP e 612 HIS 0.004 0.001 HIS e 256 Details of bonding type rmsd covalent geometry : bond 0.00429 (13572) covalent geometry : angle 0.66586 (18324) hydrogen bonds : bond 0.03921 ( 550) hydrogen bonds : angle 4.10679 ( 1617) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 337 time to evaluate : 0.547 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: P 219 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.6632 (tmm) REVERT: P 231 ARG cc_start: 0.9187 (ptp-110) cc_final: 0.8729 (ptt-90) REVERT: P 269 ARG cc_start: 0.7594 (mtm110) cc_final: 0.7165 (mpp80) REVERT: P 271 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8121 (mm-30) REVERT: P 312 LEU cc_start: 0.8080 (mp) cc_final: 0.7828 (pp) REVERT: c 19 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7339 (tp40) REVERT: c 105 ASN cc_start: 0.8779 (m-40) cc_final: 0.8483 (m110) REVERT: d 851 ARG cc_start: 0.8324 (ptm160) cc_final: 0.8099 (ptm-80) REVERT: d 868 LYS cc_start: 0.8775 (ptmm) cc_final: 0.8527 (ptmm) REVERT: d 915 GLU cc_start: 0.8213 (pt0) cc_final: 0.7974 (pt0) REVERT: d 924 LYS cc_start: 0.8370 (mttt) cc_final: 0.8061 (mttt) REVERT: d 928 TYR cc_start: 0.9084 (m-80) cc_final: 0.8644 (m-80) REVERT: d 931 ASP cc_start: 0.8269 (t0) cc_final: 0.7850 (t0) REVERT: d 932 ASP cc_start: 0.8869 (t70) cc_final: 0.8597 (t0) REVERT: e 213 MET cc_start: 0.7252 (mmm) cc_final: 0.6768 (mmm) REVERT: e 216 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7676 (pt0) REVERT: e 235 GLU cc_start: 0.9104 (tt0) cc_final: 0.8753 (tt0) REVERT: e 280 ARG cc_start: 0.8880 (ttp80) cc_final: 0.8653 (tmm160) REVERT: e 444 MET cc_start: 0.7947 (tmm) cc_final: 0.7683 (tmm) REVERT: e 492 SER cc_start: 0.9173 (OUTLIER) cc_final: 0.8750 (m) REVERT: e 515 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9047 (mm) REVERT: e 526 ARG cc_start: 0.8362 (tpp80) cc_final: 0.8000 (tpp80) REVERT: e 774 MET cc_start: 0.8785 (mmm) cc_final: 0.8416 (mmm) REVERT: f 17 GLU cc_start: 0.8276 (mp0) cc_final: 0.7947 (mp0) REVERT: f 65 LYS cc_start: 0.7845 (tptt) cc_final: 0.7371 (tppt) REVERT: f 103 GLU cc_start: 0.8400 (tt0) cc_final: 0.7892 (mp0) REVERT: i 14 LYS cc_start: 0.8567 (tttm) cc_final: 0.8222 (tppt) REVERT: i 21 GLN cc_start: 0.8304 (tp-100) cc_final: 0.7751 (tp40) REVERT: i 78 ARG cc_start: 0.5582 (OUTLIER) cc_final: 0.5079 (mmt90) REVERT: i 97 ARG cc_start: 0.8300 (ttp-110) cc_final: 0.7912 (ttp80) REVERT: i 114 ARG cc_start: 0.8665 (mtt90) cc_final: 0.8444 (mtt-85) REVERT: j 124 GLU cc_start: 0.9082 (tp30) cc_final: 0.8780 (tp30) REVERT: j 145 GLU cc_start: 0.7756 (tp30) cc_final: 0.7487 (pm20) REVERT: j 165 ASP cc_start: 0.8029 (m-30) cc_final: 0.7790 (m-30) REVERT: j 175 LYS cc_start: 0.8686 (mttt) cc_final: 0.8381 (mttm) REVERT: k 122 GLU cc_start: 0.8755 (tt0) cc_final: 0.8330 (tp30) REVERT: k 167 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8203 (tp30) REVERT: k 168 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8140 (tm-30) REVERT: k 199 GLN cc_start: 0.8656 (mm110) cc_final: 0.8442 (mm-40) REVERT: l 60 LYS cc_start: 0.9102 (tttt) cc_final: 0.6759 (ttmt) REVERT: l 78 GLU cc_start: 0.7979 (mp0) cc_final: 0.7556 (tp30) REVERT: l 81 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7727 (pt0) REVERT: l 150 GLN cc_start: 0.8798 (tt0) cc_final: 0.8364 (tt0) REVERT: m 46 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6608 (t0) REVERT: m 80 ARG cc_start: 0.7834 (mmm-85) cc_final: 0.7481 (mmm-85) outliers start: 56 outliers final: 46 residues processed: 363 average time/residue: 0.1619 time to fit residues: 77.6799 Evaluate side-chains 386 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 333 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 19 GLN Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain d residue 885 ILE Chi-restraints excluded: chain d residue 929 LYS Chi-restraints excluded: chain d residue 1055 ILE Chi-restraints excluded: chain d residue 1059 ASN Chi-restraints excluded: chain d residue 1078 LEU Chi-restraints excluded: chain d residue 1081 LYS Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 216 GLU Chi-restraints excluded: chain e residue 298 LEU Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 479 THR Chi-restraints excluded: chain e residue 492 SER Chi-restraints excluded: chain e residue 515 LEU Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 563 GLU Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 674 SER Chi-restraints excluded: chain e residue 675 LEU Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 712 ASP Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 44 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 194 THR Chi-restraints excluded: chain j residue 215 HIS Chi-restraints excluded: chain k residue 141 ILE Chi-restraints excluded: chain k residue 144 THR Chi-restraints excluded: chain k residue 173 CYS Chi-restraints excluded: chain l residue 101 GLN Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain m residue 46 ASP Chi-restraints excluded: chain m residue 81 VAL Chi-restraints excluded: chain m residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 70 optimal weight: 0.3980 chunk 44 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 1 optimal weight: 30.0000 chunk 118 optimal weight: 0.0470 chunk 157 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 137 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 71 GLN ** e 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 268 HIS ** e 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.155117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099112 restraints weight = 18293.147| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.92 r_work: 0.3094 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13572 Z= 0.139 Angle : 0.668 15.271 18324 Z= 0.330 Chirality : 0.044 0.240 2030 Planarity : 0.005 0.083 2364 Dihedral : 4.465 28.523 1807 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.95 % Allowed : 21.99 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.21), residues: 1622 helix: 1.38 (0.20), residues: 725 sheet: -1.00 (0.37), residues: 196 loop : -1.49 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG P 299 TYR 0.018 0.001 TYR P 322 PHE 0.026 0.001 PHE e 267 TRP 0.020 0.002 TRP e 330 HIS 0.004 0.001 HIS e 256 Details of bonding type rmsd covalent geometry : bond 0.00334 (13572) covalent geometry : angle 0.66762 (18324) hydrogen bonds : bond 0.03722 ( 550) hydrogen bonds : angle 4.06563 ( 1617) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 339 time to evaluate : 0.511 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: P 205 ARG cc_start: 0.6134 (mmp80) cc_final: 0.5807 (mmp80) REVERT: P 219 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.6606 (tmm) REVERT: P 231 ARG cc_start: 0.9182 (ptp-110) cc_final: 0.8869 (ptp90) REVERT: P 269 ARG cc_start: 0.7702 (mtm110) cc_final: 0.7244 (mpp80) REVERT: P 309 LYS cc_start: 0.5585 (tppt) cc_final: 0.5261 (mmmt) REVERT: P 312 LEU cc_start: 0.8060 (mp) cc_final: 0.7761 (pp) REVERT: c 19 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7294 (tp40) REVERT: c 64 ASP cc_start: 0.8834 (m-30) cc_final: 0.8432 (m-30) REVERT: c 105 ASN cc_start: 0.8784 (m-40) cc_final: 0.8482 (m110) REVERT: d 868 LYS cc_start: 0.8749 (ptmm) cc_final: 0.8496 (ptmm) REVERT: d 928 TYR cc_start: 0.9072 (m-80) cc_final: 0.8799 (m-80) REVERT: d 931 ASP cc_start: 0.8287 (t0) cc_final: 0.7869 (t0) REVERT: d 932 ASP cc_start: 0.8875 (t70) cc_final: 0.8599 (t0) REVERT: d 958 LYS cc_start: 0.9333 (tppt) cc_final: 0.9064 (tppp) REVERT: e 213 MET cc_start: 0.7238 (mmm) cc_final: 0.6772 (mmm) REVERT: e 216 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7664 (pt0) REVERT: e 235 GLU cc_start: 0.9099 (tt0) cc_final: 0.8738 (tt0) REVERT: e 280 ARG cc_start: 0.8883 (ttp80) cc_final: 0.8650 (tmm160) REVERT: e 444 MET cc_start: 0.7979 (tmm) cc_final: 0.7704 (tmm) REVERT: e 492 SER cc_start: 0.9120 (OUTLIER) cc_final: 0.8712 (m) REVERT: e 515 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8844 (mt) REVERT: e 526 ARG cc_start: 0.8359 (tpp80) cc_final: 0.7998 (tpp80) REVERT: e 634 ARG cc_start: 0.8746 (mmt-90) cc_final: 0.8484 (tpp-160) REVERT: e 774 MET cc_start: 0.8794 (mmm) cc_final: 0.8429 (mmm) REVERT: f 17 GLU cc_start: 0.8258 (mp0) cc_final: 0.7926 (mp0) REVERT: f 65 LYS cc_start: 0.7823 (tptt) cc_final: 0.7285 (tppt) REVERT: f 103 GLU cc_start: 0.8399 (tt0) cc_final: 0.7941 (mp0) REVERT: i 14 LYS cc_start: 0.8558 (tttm) cc_final: 0.8218 (tppt) REVERT: i 21 GLN cc_start: 0.8186 (tp-100) cc_final: 0.7627 (tp40) REVERT: i 78 ARG cc_start: 0.5571 (OUTLIER) cc_final: 0.5194 (mmt90) REVERT: i 114 ARG cc_start: 0.8693 (mtt90) cc_final: 0.8471 (mtt-85) REVERT: j 118 ASP cc_start: 0.8976 (m-30) cc_final: 0.8707 (p0) REVERT: j 124 GLU cc_start: 0.9066 (tp30) cc_final: 0.8690 (tp30) REVERT: j 145 GLU cc_start: 0.7752 (tp30) cc_final: 0.7462 (pm20) REVERT: j 165 ASP cc_start: 0.8019 (m-30) cc_final: 0.7783 (m-30) REVERT: j 175 LYS cc_start: 0.8678 (mttt) cc_final: 0.8381 (mttm) REVERT: k 117 GLN cc_start: 0.8325 (pp30) cc_final: 0.7924 (pp30) REVERT: k 122 GLU cc_start: 0.8760 (tt0) cc_final: 0.8328 (tp30) REVERT: k 167 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8151 (tp30) REVERT: k 168 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8195 (tm-30) REVERT: k 199 GLN cc_start: 0.8636 (mm110) cc_final: 0.8432 (mm-40) REVERT: l 60 LYS cc_start: 0.9122 (tttt) cc_final: 0.6641 (ttmt) REVERT: l 78 GLU cc_start: 0.8022 (mp0) cc_final: 0.7547 (tp30) REVERT: l 81 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7752 (pt0) REVERT: l 150 GLN cc_start: 0.8822 (tt0) cc_final: 0.8296 (tt0) REVERT: m 46 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6603 (t0) REVERT: m 80 ARG cc_start: 0.7850 (mmm-85) cc_final: 0.7502 (mmm-85) outliers start: 58 outliers final: 43 residues processed: 365 average time/residue: 0.1596 time to fit residues: 76.9436 Evaluate side-chains 382 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 332 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain c residue 19 GLN Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 96 ILE Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain d residue 860 VAL Chi-restraints excluded: chain d residue 885 ILE Chi-restraints excluded: chain d residue 929 LYS Chi-restraints excluded: chain d residue 1055 ILE Chi-restraints excluded: chain d residue 1059 ASN Chi-restraints excluded: chain d residue 1078 LEU Chi-restraints excluded: chain d residue 1081 LYS Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 216 GLU Chi-restraints excluded: chain e residue 298 LEU Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 479 THR Chi-restraints excluded: chain e residue 492 SER Chi-restraints excluded: chain e residue 515 LEU Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 563 GLU Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 674 SER Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 712 ASP Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 194 THR Chi-restraints excluded: chain j residue 215 HIS Chi-restraints excluded: chain k residue 141 ILE Chi-restraints excluded: chain k residue 144 THR Chi-restraints excluded: chain l residue 101 GLN Chi-restraints excluded: chain m residue 46 ASP Chi-restraints excluded: chain m residue 81 VAL Chi-restraints excluded: chain m residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 28 optimal weight: 3.9990 chunk 126 optimal weight: 0.0970 chunk 90 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.154092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.098034 restraints weight = 18323.056| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.91 r_work: 0.3075 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13572 Z= 0.169 Angle : 0.683 15.480 18324 Z= 0.339 Chirality : 0.045 0.221 2030 Planarity : 0.004 0.044 2364 Dihedral : 4.509 28.820 1807 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.47 % Allowed : 22.80 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.21), residues: 1622 helix: 1.38 (0.20), residues: 723 sheet: -1.01 (0.37), residues: 196 loop : -1.47 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG f 124 TYR 0.018 0.001 TYR P 322 PHE 0.025 0.001 PHE m 97 TRP 0.020 0.002 TRP e 612 HIS 0.005 0.001 HIS e 256 Details of bonding type rmsd covalent geometry : bond 0.00410 (13572) covalent geometry : angle 0.68315 (18324) hydrogen bonds : bond 0.03885 ( 550) hydrogen bonds : angle 4.09586 ( 1617) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 333 time to evaluate : 0.572 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: P 202 MET cc_start: 0.4881 (tpp) cc_final: 0.4617 (tpt) REVERT: P 219 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.6613 (tmm) REVERT: P 231 ARG cc_start: 0.9190 (ptp-110) cc_final: 0.8865 (ptp90) REVERT: P 269 ARG cc_start: 0.7772 (mtm110) cc_final: 0.7325 (mpp80) REVERT: P 271 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8053 (mm-30) REVERT: P 309 LYS cc_start: 0.5884 (tppt) cc_final: 0.5549 (mmmt) REVERT: P 312 LEU cc_start: 0.8019 (mp) cc_final: 0.7735 (pp) REVERT: c 19 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7326 (tp40) REVERT: c 51 ARG cc_start: 0.8212 (mtt180) cc_final: 0.7936 (mtt180) REVERT: c 105 ASN cc_start: 0.8763 (m-40) cc_final: 0.8480 (m110) REVERT: d 868 LYS cc_start: 0.8693 (ptmm) cc_final: 0.8455 (ptmm) REVERT: d 928 TYR cc_start: 0.9084 (m-80) cc_final: 0.8649 (m-80) REVERT: d 931 ASP cc_start: 0.8304 (t0) cc_final: 0.7883 (t0) REVERT: d 932 ASP cc_start: 0.8881 (t70) cc_final: 0.8599 (t0) REVERT: d 958 LYS cc_start: 0.9338 (tppt) cc_final: 0.9039 (tppp) REVERT: e 213 MET cc_start: 0.7244 (mmm) cc_final: 0.6766 (mmm) REVERT: e 216 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7739 (pt0) REVERT: e 235 GLU cc_start: 0.9150 (tt0) cc_final: 0.8797 (tt0) REVERT: e 425 ASN cc_start: 0.9181 (t0) cc_final: 0.8758 (t0) REVERT: e 444 MET cc_start: 0.8007 (tmm) cc_final: 0.7726 (tmm) REVERT: e 480 ASP cc_start: 0.8447 (t0) cc_final: 0.8230 (t0) REVERT: e 492 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8742 (m) REVERT: e 515 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8874 (mt) REVERT: e 526 ARG cc_start: 0.8493 (tpp80) cc_final: 0.8121 (tpp80) REVERT: e 774 MET cc_start: 0.8839 (mmm) cc_final: 0.8483 (mmm) REVERT: f 17 GLU cc_start: 0.8273 (mp0) cc_final: 0.7945 (mp0) REVERT: f 65 LYS cc_start: 0.7859 (tptt) cc_final: 0.7380 (tppt) REVERT: f 103 GLU cc_start: 0.8392 (tt0) cc_final: 0.7939 (mp0) REVERT: i 14 LYS cc_start: 0.8561 (tttm) cc_final: 0.8214 (tppt) REVERT: i 21 GLN cc_start: 0.8255 (tp-100) cc_final: 0.7709 (tp40) REVERT: i 78 ARG cc_start: 0.5659 (OUTLIER) cc_final: 0.5167 (mmt90) REVERT: i 114 ARG cc_start: 0.8691 (mtt90) cc_final: 0.8473 (mtt-85) REVERT: j 118 ASP cc_start: 0.8964 (m-30) cc_final: 0.8722 (p0) REVERT: j 124 GLU cc_start: 0.9070 (tp30) cc_final: 0.8653 (tp30) REVERT: j 145 GLU cc_start: 0.7745 (tp30) cc_final: 0.7488 (pm20) REVERT: j 165 ASP cc_start: 0.8035 (m-30) cc_final: 0.7800 (m-30) REVERT: j 175 LYS cc_start: 0.8697 (mttt) cc_final: 0.8396 (mttm) REVERT: k 117 GLN cc_start: 0.8360 (pp30) cc_final: 0.7955 (pp30) REVERT: k 122 GLU cc_start: 0.8769 (tt0) cc_final: 0.8359 (tp30) REVERT: k 167 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8181 (tp30) REVERT: k 168 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8157 (tm-30) REVERT: k 199 GLN cc_start: 0.8667 (mm110) cc_final: 0.8461 (mm-40) REVERT: l 60 LYS cc_start: 0.9096 (tttt) cc_final: 0.6760 (ttmt) REVERT: l 78 GLU cc_start: 0.8037 (mp0) cc_final: 0.7570 (tp30) REVERT: l 81 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7779 (pt0) REVERT: m 46 ASP cc_start: 0.6959 (OUTLIER) cc_final: 0.6425 (t0) REVERT: m 80 ARG cc_start: 0.7890 (mmm-85) cc_final: 0.7558 (mmm-85) outliers start: 51 outliers final: 42 residues processed: 357 average time/residue: 0.1631 time to fit residues: 77.3469 Evaluate side-chains 375 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 326 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 219 MET Chi-restraints excluded: chain P residue 236 LYS Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain c residue 19 GLN Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain d residue 860 VAL Chi-restraints excluded: chain d residue 885 ILE Chi-restraints excluded: chain d residue 920 THR Chi-restraints excluded: chain d residue 929 LYS Chi-restraints excluded: chain d residue 1055 ILE Chi-restraints excluded: chain d residue 1059 ASN Chi-restraints excluded: chain d residue 1078 LEU Chi-restraints excluded: chain e residue 205 TYR Chi-restraints excluded: chain e residue 216 GLU Chi-restraints excluded: chain e residue 298 LEU Chi-restraints excluded: chain e residue 476 VAL Chi-restraints excluded: chain e residue 479 THR Chi-restraints excluded: chain e residue 492 SER Chi-restraints excluded: chain e residue 515 LEU Chi-restraints excluded: chain e residue 546 VAL Chi-restraints excluded: chain e residue 563 GLU Chi-restraints excluded: chain e residue 612 TRP Chi-restraints excluded: chain e residue 632 CYS Chi-restraints excluded: chain e residue 674 SER Chi-restraints excluded: chain e residue 700 HIS Chi-restraints excluded: chain e residue 712 ASP Chi-restraints excluded: chain e residue 778 THR Chi-restraints excluded: chain e residue 786 THR Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 44 SER Chi-restraints excluded: chain i residue 29 THR Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 78 ARG Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 194 THR Chi-restraints excluded: chain j residue 215 HIS Chi-restraints excluded: chain k residue 141 ILE Chi-restraints excluded: chain k residue 144 THR Chi-restraints excluded: chain l residue 101 GLN Chi-restraints excluded: chain l residue 109 SER Chi-restraints excluded: chain m residue 46 ASP Chi-restraints excluded: chain m residue 81 VAL Chi-restraints excluded: chain m residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 104 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 27 GLN ** e 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.154007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098018 restraints weight = 18353.959| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.91 r_work: 0.3076 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13572 Z= 0.168 Angle : 0.692 15.504 18324 Z= 0.343 Chirality : 0.044 0.234 2030 Planarity : 0.005 0.043 2364 Dihedral : 4.525 28.807 1807 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.81 % Allowed : 22.80 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.21), residues: 1622 helix: 1.35 (0.20), residues: 732 sheet: -1.03 (0.37), residues: 196 loop : -1.47 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 299 TYR 0.016 0.001 TYR P 322 PHE 0.021 0.001 PHE e 267 TRP 0.024 0.002 TRP e 330 HIS 0.005 0.001 HIS e 256 Details of bonding type rmsd covalent geometry : bond 0.00408 (13572) covalent geometry : angle 0.69174 (18324) hydrogen bonds : bond 0.03836 ( 550) hydrogen bonds : angle 4.07394 ( 1617) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3986.94 seconds wall clock time: 68 minutes 52.28 seconds (4132.28 seconds total)