Starting phenix.real_space_refine on Thu Jul 31 05:36:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7egf_31115/07_2025/7egf_31115.cif Found real_map, /net/cci-nas-00/data/ceres_data/7egf_31115/07_2025/7egf_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_31115/07_2025/7egf_31115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7egf_31115/07_2025/7egf_31115.map" model { file = "/net/cci-nas-00/data/ceres_data/7egf_31115/07_2025/7egf_31115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7egf_31115/07_2025/7egf_31115.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.30, per 1000 atoms: 0.62 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: 2.81 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.25 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: 3.70 Time building geometry restraints manager: 3.43 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 30.760 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.890 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.002 TRP e 612 HIS 0.007 0.001 HIS e 584 PHE 0.025 0.002 PHE e 600 TYR 0.027 0.002 TYR j 216 ARG 0.009 0.000 ARG e 682 Details of bonding type rmsd hydrogen bonds : bond 0.24232 ( 550) hydrogen bonds : angle 8.79011 ( 1617) covalent geometry : bond 0.00774 (13572) covalent geometry : angle 1.06515 (18324) *********************** 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 : 1.477 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: 0.7376 (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: 0.7187 (ttt) outliers start: 31 outliers final: 9 residues processed: 438 average time/residue: 0.3914 time to fit residues: 226.2899 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 : 1.552 ------------------------------------------------------------------------------- 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 134 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.156324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100227 restraints weight = 18084.006| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.90 r_work: 0.3103 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2794 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= 0.186 Angle : 0.700 12.286 18324 Z= 0.357 Chirality : 0.045 0.255 2030 Planarity : 0.006 0.055 2364 Dihedral : 5.987 49.173 1830 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.31 % Allowed : 15.79 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.20), residues: 1622 helix: -0.28 (0.19), residues: 715 sheet: -1.84 (0.36), residues: 188 loop : -2.18 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP e 612 HIS 0.006 0.001 HIS l 119 PHE 0.020 0.002 PHE e 264 TYR 0.021 0.002 TYR j 216 ARG 0.011 0.001 ARG e 280 Details of bonding type rmsd hydrogen bonds : bond 0.05369 ( 550) hydrogen bonds : angle 4.87784 ( 1617) covalent geometry : bond 0.00426 (13572) covalent geometry : angle 0.69967 (18324) *********************** 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 405 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 371 time to evaluate : 3.019 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 202 MET cc_start: 0.4792 (ttt) cc_final: 0.4506 (tpp) REVERT: c 36 ASP cc_start: 0.8797 (t0) cc_final: 0.8313 (t0) REVERT: c 81 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7934 (mm-30) REVERT: c 84 ILE cc_start: 0.8300 (tt) cc_final: 0.8045 (tt) REVERT: c 105 ASN cc_start: 0.8747 (m-40) cc_final: 0.8505 (m110) REVERT: d 851 ARG cc_start: 0.8372 (mtp-110) cc_final: 0.8131 (ptm160) REVERT: d 958 LYS cc_start: 0.9422 (tppt) cc_final: 0.9130 (tppt) REVERT: e 216 GLU cc_start: 0.7702 (pt0) cc_final: 0.7348 (pt0) REVERT: e 265 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8164 (tp30) REVERT: e 328 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8327 (tt0) REVERT: e 444 MET cc_start: 0.8029 (tmm) cc_final: 0.7815 (tmm) REVERT: e 526 ARG cc_start: 0.8411 (tpp80) cc_final: 0.7869 (tpp80) REVERT: f 17 GLU cc_start: 0.8450 (mp0) cc_final: 0.8181 (mp0) REVERT: i 97 ARG cc_start: 0.8654 (ttp-170) cc_final: 0.8201 (ttp80) REVERT: i 110 TYR cc_start: 0.8781 (m-80) cc_final: 0.8021 (m-10) REVERT: j 118 ASP cc_start: 0.9068 (m-30) cc_final: 0.8788 (m-30) REVERT: j 122 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: j 175 LYS cc_start: 0.8781 (mttt) cc_final: 0.8406 (mttp) REVERT: k 123 MET cc_start: 0.9121 (mmm) cc_final: 0.8724 (mmt) REVERT: k 144 THR cc_start: 0.7192 (OUTLIER) cc_final: 0.6901 (t) REVERT: k 164 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8556 (mt-10) REVERT: l 56 GLN cc_start: 0.7868 (pt0) cc_final: 0.6927 (mp10) REVERT: l 64 GLN cc_start: 0.8044 (tp40) cc_final: 0.7789 (tp40) REVERT: l 81 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8005 (pt0) REVERT: l 150 GLN cc_start: 0.8870 (tt0) cc_final: 0.8662 (tt0) REVERT: m 80 ARG cc_start: 0.7762 (mmm-85) cc_final: 0.7425 (mmm-85) REVERT: m 102 ASP cc_start: 0.8201 (m-30) cc_final: 0.7891 (t0) outliers start: 34 outliers final: 20 residues processed: 386 average time/residue: 0.4022 time to fit residues: 208.4583 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 : 1.556 ------------------------------------------------------------------------------- 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 36 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 2 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 327 ASN c 43 GLN ** 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 = 0.3986 r_free = 0.3986 target = 0.155017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.099667 restraints weight = 18458.204| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.90 r_work: 0.3110 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13572 Z= 0.168 Angle : 0.649 11.992 18324 Z= 0.326 Chirality : 0.044 0.212 2030 Planarity : 0.005 0.056 2364 Dihedral : 5.137 45.294 1812 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.86 % Allowed : 17.09 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.20), residues: 1622 helix: 0.45 (0.19), residues: 716 sheet: -1.57 (0.36), residues: 190 loop : -1.89 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP e 612 HIS 0.007 0.001 HIS e 256 PHE 0.015 0.002 PHE e 264 TYR 0.021 0.002 TYR e 275 ARG 0.008 0.001 ARG f 124 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 550) hydrogen bonds : angle 4.44643 ( 1617) covalent geometry : bond 0.00391 (13572) covalent geometry : angle 0.64929 (18324) *********************** 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 398 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 356 time to evaluate : 1.534 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 202 MET cc_start: 0.4976 (ttt) cc_final: 0.4684 (tpp) REVERT: P 219 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6290 (tmm) REVERT: P 231 ARG cc_start: 0.9297 (ptp-110) cc_final: 0.8881 (ptt-90) REVERT: P 299 ARG cc_start: 0.9653 (mmm-85) cc_final: 0.9360 (mmp80) REVERT: P 312 LEU cc_start: 0.8061 (mp) cc_final: 0.7844 (pp) REVERT: P 322 TYR cc_start: 0.9122 (m-10) cc_final: 0.8912 (m-10) REVERT: c 105 ASN cc_start: 0.8628 (m-40) cc_final: 0.8205 (m110) REVERT: d 924 LYS cc_start: 0.8380 (mttt) cc_final: 0.8058 (mttt) REVERT: d 931 ASP cc_start: 0.8162 (t0) cc_final: 0.7902 (t0) REVERT: d 958 LYS cc_start: 0.9413 (tppt) cc_final: 0.9103 (tppt) REVERT: e 213 MET cc_start: 0.7242 (mmm) cc_final: 0.7009 (mmm) REVERT: e 216 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7562 (pt0) REVERT: e 235 GLU cc_start: 0.8995 (tt0) cc_final: 0.8702 (tt0) REVERT: e 265 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8258 (tp30) REVERT: e 278 ASP cc_start: 0.7889 (m-30) cc_final: 0.7650 (m-30) REVERT: e 444 MET cc_start: 0.8081 (tmm) cc_final: 0.7851 (tmm) REVERT: e 526 ARG cc_start: 0.8468 (tpp80) cc_final: 0.7891 (tpp80) REVERT: e 774 MET cc_start: 0.8701 (mmm) cc_final: 0.8408 (mmm) REVERT: e 787 ARG cc_start: 0.8364 (mmm160) cc_final: 0.7840 (mmm-85) REVERT: f 17 GLU cc_start: 0.8393 (mp0) cc_final: 0.8095 (mp0) REVERT: i 21 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7666 (tp40) REVERT: i 62 LYS cc_start: 0.9165 (mtmm) cc_final: 0.8939 (mtpp) REVERT: i 97 ARG cc_start: 0.8503 (ttp-110) cc_final: 0.8219 (ttp80) REVERT: i 110 TYR cc_start: 0.8883 (m-80) cc_final: 0.8117 (m-10) REVERT: i 130 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8360 (mtpt) REVERT: j 118 ASP cc_start: 0.9012 (m-30) cc_final: 0.8744 (m-30) REVERT: j 175 LYS cc_start: 0.8818 (mttt) cc_final: 0.8418 (mttp) REVERT: k 139 GLN cc_start: 0.8775 (mt0) cc_final: 0.8437 (mm-40) REVERT: k 164 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8389 (mt-10) REVERT: k 167 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8108 (tp30) REVERT: k 168 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8193 (tm-30) REVERT: l 60 LYS cc_start: 0.9107 (tttt) cc_final: 0.7018 (ttmm) REVERT: l 64 GLN cc_start: 0.7988 (tp40) cc_final: 0.7753 (tp40) REVERT: l 78 GLU cc_start: 0.7981 (mp0) cc_final: 0.7575 (tp30) REVERT: l 81 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7880 (pt0) REVERT: l 150 GLN cc_start: 0.8884 (tt0) cc_final: 0.8660 (tt0) REVERT: m 30 ARG cc_start: 0.8450 (mmt180) cc_final: 0.7872 (mmt180) REVERT: m 90 ILE cc_start: 0.8606 (tp) cc_final: 0.8403 (tp) outliers start: 42 outliers final: 27 residues processed: 374 average time/residue: 0.3906 time to fit residues: 194.3037 Evaluate side-chains 367 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 337 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 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 d residue 929 LYS 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 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 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 26 MET Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 130 LYS Chi-restraints excluded: chain k residue 140 SER Chi-restraints excluded: chain k residue 155 SER Chi-restraints excluded: chain k residue 173 CYS 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 124 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 256 GLN ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 126 ASN j 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.152858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.096694 restraints weight = 18281.941| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.90 r_work: 0.3055 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13572 Z= 0.230 Angle : 0.678 13.984 18324 Z= 0.341 Chirality : 0.046 0.219 2030 Planarity : 0.005 0.046 2364 Dihedral : 5.056 43.691 1809 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.81 % Allowed : 17.90 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.21), residues: 1622 helix: 0.65 (0.19), residues: 723 sheet: -1.58 (0.36), residues: 192 loop : -1.74 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP e 612 HIS 0.009 0.001 HIS e 256 PHE 0.016 0.002 PHE e 264 TYR 0.027 0.002 TYR e 275 ARG 0.009 0.001 ARG f 124 Details of bonding type rmsd hydrogen bonds : bond 0.04510 ( 550) hydrogen bonds : angle 4.38140 ( 1617) covalent geometry : bond 0.00550 (13572) covalent geometry : angle 0.67778 (18324) *********************** 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 399 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 343 time to evaluate : 1.815 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: 0.5232 (ttt) cc_final: 0.5011 (tpp) REVERT: P 219 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.6360 (tmm) REVERT: P 269 ARG cc_start: 0.7733 (mtm110) cc_final: 0.6160 (mtm110) REVERT: P 299 ARG cc_start: 0.9671 (mmm-85) cc_final: 0.9354 (mmp80) REVERT: P 316 LYS cc_start: 0.9647 (mmmm) cc_final: 0.9386 (mmmt) REVERT: c 27 GLN cc_start: 0.8524 (tt0) cc_final: 0.8323 (tt0) REVERT: c 88 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8074 (tm-30) REVERT: c 105 ASN cc_start: 0.8694 (m-40) cc_final: 0.8334 (m110) REVERT: d 931 ASP cc_start: 0.8172 (t0) cc_final: 0.7842 (t0) REVERT: d 958 LYS cc_start: 0.9365 (tppt) cc_final: 0.9072 (tppt) REVERT: d 963 ARG cc_start: 0.8690 (ptt-90) cc_final: 0.8364 (ptp-170) REVERT: e 210 ASP cc_start: 0.8449 (m-30) cc_final: 0.7454 (t0) REVERT: e 213 MET cc_start: 0.7307 (mmm) cc_final: 0.6539 (mmm) REVERT: e 216 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7610 (pt0) REVERT: e 235 GLU cc_start: 0.9067 (tt0) cc_final: 0.8737 (tt0) REVERT: e 265 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8314 (tp30) REVERT: e 268 HIS cc_start: 0.8313 (p90) cc_final: 0.7996 (p90) REVERT: e 280 ARG cc_start: 0.8865 (ttp80) cc_final: 0.8645 (tmm160) REVERT: e 444 MET cc_start: 0.8039 (tmm) cc_final: 0.7803 (tmm) REVERT: e 774 MET cc_start: 0.8717 (mmm) cc_final: 0.8385 (mmm) REVERT: f 17 GLU cc_start: 0.8414 (mp0) cc_final: 0.8109 (mp0) REVERT: f 65 LYS cc_start: 0.7885 (tptt) cc_final: 0.7237 (tppt) REVERT: i 21 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7640 (tp40) REVERT: i 62 LYS cc_start: 0.9174 (mtmm) cc_final: 0.8958 (mtpp) REVERT: j 118 ASP cc_start: 0.9058 (m-30) cc_final: 0.8735 (m-30) REVERT: j 175 LYS cc_start: 0.8795 (mttt) cc_final: 0.8475 (mttm) REVERT: k 139 GLN cc_start: 0.8797 (mt0) cc_final: 0.8379 (mm-40) REVERT: k 167 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8160 (tp30) REVERT: k 168 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8231 (tm-30) REVERT: l 60 LYS cc_start: 0.9128 (tttt) cc_final: 0.6937 (ttmm) REVERT: l 64 GLN cc_start: 0.8026 (tp40) cc_final: 0.7818 (tp40) REVERT: l 78 GLU cc_start: 0.7993 (mp0) cc_final: 0.7551 (tp30) REVERT: l 81 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7645 (pt0) REVERT: m 30 ARG cc_start: 0.8442 (mmt180) cc_final: 0.7923 (mmt180) REVERT: m 90 ILE cc_start: 0.8579 (tp) cc_final: 0.8336 (tp) outliers start: 56 outliers final: 43 residues processed: 365 average time/residue: 0.3610 time to fit residues: 174.5355 Evaluate side-chains 378 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 333 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 12 VAL Chi-restraints excluded: chain c residue 26 VAL 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 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 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 80 VAL Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 102 THR 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 109 SER 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 89 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 58 optimal weight: 0.0050 chunk 59 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 290 HIS ** 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 = 0.3963 r_free = 0.3963 target = 0.153614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.097553 restraints weight = 18431.697| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.92 r_work: 0.3067 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13572 Z= 0.179 Angle : 0.647 13.514 18324 Z= 0.323 Chirality : 0.044 0.224 2030 Planarity : 0.005 0.119 2364 Dihedral : 4.802 29.354 1807 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.74 % Allowed : 19.67 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1622 helix: 0.87 (0.19), residues: 732 sheet: -1.33 (0.36), residues: 197 loop : -1.69 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP e 612 HIS 0.008 0.001 HIS e 290 PHE 0.031 0.002 PHE P 335 TYR 0.021 0.002 TYR e 275 ARG 0.012 0.001 ARG P 208 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 550) hydrogen bonds : angle 4.22158 ( 1617) covalent geometry : bond 0.00427 (13572) covalent geometry : angle 0.64653 (18324) *********************** 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 395 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 340 time to evaluate : 3.359 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: 0.7539 (OUTLIER) cc_final: 0.6423 (tmm) REVERT: P 231 ARG cc_start: 0.9294 (ptp-110) cc_final: 0.9031 (ptp90) REVERT: P 299 ARG cc_start: 0.9664 (mmm-85) cc_final: 0.9449 (mmp80) REVERT: c 19 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7358 (tp40) REVERT: c 27 GLN cc_start: 0.8548 (tt0) cc_final: 0.8335 (tt0) REVERT: c 89 PRO cc_start: 0.9051 (Cg_exo) cc_final: 0.8743 (Cg_endo) REVERT: c 105 ASN cc_start: 0.8736 (m-40) cc_final: 0.8377 (m110) REVERT: d 931 ASP cc_start: 0.8129 (t0) cc_final: 0.7750 (t0) REVERT: d 963 ARG cc_start: 0.8788 (ptt-90) cc_final: 0.8583 (ptp-170) REVERT: e 213 MET cc_start: 0.7232 (mmm) cc_final: 0.6991 (mmm) REVERT: e 216 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: e 235 GLU cc_start: 0.9075 (tt0) cc_final: 0.8737 (tt0) REVERT: e 268 HIS cc_start: 0.8276 (OUTLIER) cc_final: 0.7998 (p90) REVERT: e 318 LYS cc_start: 0.8392 (tttt) cc_final: 0.8052 (tmtt) REVERT: e 319 ARG cc_start: 0.8675 (ptp-110) cc_final: 0.8470 (ptp90) REVERT: e 444 MET cc_start: 0.8035 (tmm) cc_final: 0.7799 (tmm) REVERT: e 449 LYS cc_start: 0.8736 (mtmt) cc_final: 0.7988 (tptt) REVERT: e 515 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8960 (mm) REVERT: e 526 ARG cc_start: 0.8319 (tpp80) cc_final: 0.7917 (tpp80) REVERT: e 774 MET cc_start: 0.8752 (mmm) cc_final: 0.8412 (mmm) REVERT: f 17 GLU cc_start: 0.8360 (mp0) cc_final: 0.8062 (mp0) REVERT: f 65 LYS cc_start: 0.7891 (tptt) cc_final: 0.7291 (tppt) REVERT: f 103 GLU cc_start: 0.8383 (tt0) cc_final: 0.7836 (mp0) REVERT: i 21 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7651 (tp40) REVERT: i 62 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8966 (mtpp) REVERT: i 97 ARG cc_start: 0.8531 (ttm110) cc_final: 0.8071 (ttp80) REVERT: j 118 ASP cc_start: 0.9083 (m-30) cc_final: 0.8848 (m-30) REVERT: j 124 GLU cc_start: 0.9087 (tp30) cc_final: 0.8662 (tp30) REVERT: j 175 LYS cc_start: 0.8710 (mttt) cc_final: 0.8393 (mttm) REVERT: k 139 GLN cc_start: 0.8754 (mt0) cc_final: 0.8429 (mm-40) REVERT: k 167 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8154 (tp30) REVERT: k 168 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8195 (tm-30) REVERT: l 60 LYS cc_start: 0.9149 (tttt) cc_final: 0.6881 (ttmm) REVERT: l 64 GLN cc_start: 0.8041 (tp40) cc_final: 0.7837 (tp40) REVERT: l 78 GLU cc_start: 0.7985 (mp0) cc_final: 0.7521 (tp30) REVERT: l 81 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7630 (pt0) REVERT: m 30 ARG cc_start: 0.8383 (mmt180) cc_final: 0.7838 (mmt180) outliers start: 55 outliers final: 39 residues processed: 364 average time/residue: 0.4884 time to fit residues: 239.4832 Evaluate side-chains 377 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 333 time to evaluate : 2.659 ------------------------------------------------------------------------------- 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 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 c residue 107 LEU 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 216 GLU Chi-restraints excluded: chain e residue 268 HIS 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 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 56 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain j residue 194 THR 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 109 SER Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain m residue 81 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 118 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 636 HIS ** 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 = 0.154389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.098642 restraints weight = 18477.366| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.91 r_work: 0.3084 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4055 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= 0.152 Angle : 0.646 14.662 18324 Z= 0.317 Chirality : 0.043 0.211 2030 Planarity : 0.004 0.044 2364 Dihedral : 4.648 28.824 1807 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.15 % Allowed : 20.15 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1622 helix: 1.13 (0.20), residues: 730 sheet: -1.22 (0.36), residues: 197 loop : -1.64 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP e 612 HIS 0.004 0.001 HIS e 256 PHE 0.034 0.002 PHE e 267 TYR 0.037 0.002 TYR e 275 ARG 0.010 0.001 ARG f 124 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 550) hydrogen bonds : angle 4.08572 ( 1617) covalent geometry : bond 0.00364 (13572) covalent geometry : angle 0.64596 (18324) *********************** 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 404 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 343 time to evaluate : 1.798 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: 0.5125 (tpp) cc_final: 0.4813 (tpt) REVERT: P 219 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.6548 (tmm) REVERT: P 231 ARG cc_start: 0.9226 (ptp-110) cc_final: 0.8877 (ptp-170) REVERT: P 299 ARG cc_start: 0.9651 (mmm-85) cc_final: 0.9408 (mmp80) REVERT: c 19 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7384 (tp40) REVERT: c 27 GLN cc_start: 0.8561 (tt0) cc_final: 0.8286 (tt0) REVERT: c 105 ASN cc_start: 0.8758 (m-40) cc_final: 0.8432 (m110) REVERT: d 915 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7979 (pt0) REVERT: d 931 ASP cc_start: 0.8214 (t0) cc_final: 0.7833 (t0) REVERT: d 958 LYS cc_start: 0.9362 (tppt) cc_final: 0.8939 (tppp) REVERT: e 213 MET cc_start: 0.7192 (mmm) cc_final: 0.6944 (mmm) REVERT: e 216 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7604 (pt0) REVERT: e 235 GLU cc_start: 0.9119 (tt0) cc_final: 0.8800 (tt0) REVERT: e 280 ARG cc_start: 0.8853 (ttp80) cc_final: 0.8637 (tmm160) REVERT: e 319 ARG cc_start: 0.8709 (ptp-110) cc_final: 0.8419 (ptp90) REVERT: e 425 ASN cc_start: 0.9201 (t0) cc_final: 0.8729 (t0) REVERT: e 444 MET cc_start: 0.8002 (tmm) cc_final: 0.7754 (tmm) REVERT: e 515 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9007 (mm) REVERT: e 526 ARG cc_start: 0.8345 (tpp80) cc_final: 0.7949 (tpp80) REVERT: e 554 ASP cc_start: 0.8378 (p0) cc_final: 0.8050 (p0) REVERT: e 634 ARG cc_start: 0.8767 (mmt-90) cc_final: 0.8494 (tpp-160) REVERT: e 774 MET cc_start: 0.8808 (mmm) cc_final: 0.8467 (mmm) REVERT: e 788 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7834 (mtt180) REVERT: f 17 GLU cc_start: 0.8367 (mp0) cc_final: 0.8072 (mp0) REVERT: f 65 LYS cc_start: 0.7895 (tptt) cc_final: 0.7381 (tppt) REVERT: f 103 GLU cc_start: 0.8363 (tt0) cc_final: 0.7916 (mp0) REVERT: i 14 LYS cc_start: 0.8450 (tttm) cc_final: 0.8137 (tppt) REVERT: i 21 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7685 (tp40) REVERT: i 78 ARG cc_start: 0.5543 (OUTLIER) cc_final: 0.5106 (mmt90) REVERT: i 97 ARG cc_start: 0.8503 (ttm110) cc_final: 0.8274 (ttp80) REVERT: j 118 ASP cc_start: 0.9074 (m-30) cc_final: 0.8865 (m-30) REVERT: j 124 GLU cc_start: 0.9059 (tp30) cc_final: 0.8704 (tp30) REVERT: j 126 TYR cc_start: 0.8391 (t80) cc_final: 0.8157 (t80) REVERT: j 175 LYS cc_start: 0.8746 (mttt) cc_final: 0.8441 (mttm) REVERT: k 167 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8223 (tp30) REVERT: k 193 ARG cc_start: 0.8665 (ttm-80) cc_final: 0.8424 (ttm-80) REVERT: k 199 GLN cc_start: 0.8636 (mm110) cc_final: 0.8395 (mm-40) REVERT: l 60 LYS cc_start: 0.9115 (tttt) cc_final: 0.6721 (ttmm) REVERT: l 64 GLN cc_start: 0.8065 (tp40) cc_final: 0.7859 (tp40) REVERT: l 78 GLU cc_start: 0.7953 (mp0) cc_final: 0.7524 (tp30) REVERT: l 81 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7600 (pt0) REVERT: l 150 GLN cc_start: 0.8902 (tt0) cc_final: 0.8372 (tt0) REVERT: m 73 MET cc_start: 0.8215 (mtp) cc_final: 0.7989 (mtm) outliers start: 61 outliers final: 43 residues processed: 370 average time/residue: 0.4824 time to fit residues: 235.3234 Evaluate side-chains 381 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 331 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 915 GLU 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 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 e residue 788 ARG 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 f residue 76 LYS 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 194 THR Chi-restraints excluded: chain k residue 145 SER Chi-restraints excluded: chain k residue 173 CYS 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 60 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 150 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 167 ASN d 936 GLN ** e 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 636 HIS ** 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 = 0.3980 r_free = 0.3980 target = 0.154812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099077 restraints weight = 18333.416| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.90 r_work: 0.3091 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13572 Z= 0.148 Angle : 0.653 14.832 18324 Z= 0.322 Chirality : 0.044 0.248 2030 Planarity : 0.005 0.056 2364 Dihedral : 4.568 28.681 1807 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.61 % Allowed : 21.03 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1622 helix: 1.27 (0.20), residues: 723 sheet: -1.14 (0.36), residues: 195 loop : -1.56 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP e 330 HIS 0.004 0.001 HIS e 256 PHE 0.048 0.002 PHE e 267 TYR 0.020 0.001 TYR e 275 ARG 0.010 0.001 ARG f 124 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 550) hydrogen bonds : angle 4.08308 ( 1617) covalent geometry : bond 0.00356 (13572) covalent geometry : angle 0.65251 (18324) *********************** 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 400 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 347 time to evaluate : 1.674 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 202 MET cc_start: 0.5364 (tpp) cc_final: 0.5073 (tpt) REVERT: P 219 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.6608 (tmm) REVERT: P 269 ARG cc_start: 0.7451 (mtm180) cc_final: 0.7218 (mtm-85) REVERT: P 271 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8292 (mm-30) REVERT: P 299 ARG cc_start: 0.9643 (mmm-85) cc_final: 0.9413 (mmp80) REVERT: P 312 LEU cc_start: 0.8020 (pt) cc_final: 0.7687 (mp) REVERT: P 318 ARG cc_start: 0.9081 (tmm160) cc_final: 0.8811 (ttp80) REVERT: P 336 ARG cc_start: 0.7679 (mmm160) cc_final: 0.7433 (mmm160) REVERT: c 19 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7346 (tp40) REVERT: c 27 GLN cc_start: 0.8547 (tt0) cc_final: 0.8259 (tt0) REVERT: c 88 GLU cc_start: 0.8356 (tp30) cc_final: 0.8100 (tp30) REVERT: c 105 ASN cc_start: 0.8774 (m-40) cc_final: 0.8461 (m110) REVERT: d 851 ARG cc_start: 0.8122 (ptm160) cc_final: 0.7919 (ptm-80) REVERT: d 868 LYS cc_start: 0.8775 (ptmm) cc_final: 0.8542 (ptmm) REVERT: d 915 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7995 (pt0) REVERT: d 931 ASP cc_start: 0.8267 (t0) cc_final: 0.7889 (t0) REVERT: d 932 ASP cc_start: 0.8869 (t70) cc_final: 0.8609 (t0) REVERT: d 958 LYS cc_start: 0.9298 (tppt) cc_final: 0.8992 (tppp) REVERT: e 213 MET cc_start: 0.7177 (mmm) cc_final: 0.6929 (mmm) REVERT: e 216 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7598 (pt0) REVERT: e 235 GLU cc_start: 0.9127 (tt0) cc_final: 0.8794 (tt0) REVERT: e 318 LYS cc_start: 0.8411 (tttt) cc_final: 0.8028 (tmtt) REVERT: e 319 ARG cc_start: 0.8719 (ptp-110) cc_final: 0.8442 (ptp90) REVERT: e 336 HIS cc_start: 0.8782 (m90) cc_final: 0.8572 (m170) REVERT: e 425 ASN cc_start: 0.9212 (t0) cc_final: 0.8725 (t0) REVERT: e 444 MET cc_start: 0.7998 (tmm) cc_final: 0.7726 (tmm) REVERT: e 515 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9021 (mm) REVERT: e 526 ARG cc_start: 0.8352 (tpp80) cc_final: 0.7978 (tpp80) REVERT: e 554 ASP cc_start: 0.8332 (p0) cc_final: 0.7920 (p0) REVERT: e 634 ARG cc_start: 0.8763 (mmt-90) cc_final: 0.8493 (tpp-160) REVERT: e 774 MET cc_start: 0.8788 (mmm) cc_final: 0.8442 (mmm) REVERT: e 788 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7379 (mtt180) REVERT: f 17 GLU cc_start: 0.8328 (mp0) cc_final: 0.8010 (mp0) REVERT: f 65 LYS cc_start: 0.7877 (tptt) cc_final: 0.7368 (tppt) REVERT: f 103 GLU cc_start: 0.8413 (tt0) cc_final: 0.7974 (mp0) REVERT: i 14 LYS cc_start: 0.8459 (tttm) cc_final: 0.8130 (tppt) REVERT: i 21 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7714 (tp40) REVERT: i 97 ARG cc_start: 0.8460 (ttm110) cc_final: 0.8212 (ttp80) REVERT: j 118 ASP cc_start: 0.9067 (m-30) cc_final: 0.8864 (m-30) REVERT: j 124 GLU cc_start: 0.9100 (tp30) cc_final: 0.8756 (tp30) REVERT: j 165 ASP cc_start: 0.8033 (m-30) cc_final: 0.7798 (m-30) REVERT: j 175 LYS cc_start: 0.8729 (mttt) cc_final: 0.8429 (mttm) REVERT: k 122 GLU cc_start: 0.8722 (tt0) cc_final: 0.8361 (tp30) REVERT: k 167 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8207 (tp30) REVERT: k 168 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8090 (tm-30) REVERT: k 193 ARG cc_start: 0.8677 (ttm-80) cc_final: 0.8416 (ttm-80) REVERT: k 199 GLN cc_start: 0.8632 (mm110) cc_final: 0.8403 (mm-40) REVERT: l 60 LYS cc_start: 0.9068 (tttt) cc_final: 0.8559 (tttt) REVERT: l 64 GLN cc_start: 0.8059 (tp40) cc_final: 0.7787 (tp40) REVERT: l 78 GLU cc_start: 0.7934 (mp0) cc_final: 0.7709 (tp30) REVERT: l 150 GLN cc_start: 0.8847 (tt0) cc_final: 0.8280 (tt0) REVERT: m 80 ARG cc_start: 0.7847 (mmm-85) cc_final: 0.7463 (mmm-85) outliers start: 53 outliers final: 41 residues processed: 373 average time/residue: 0.3484 time to fit residues: 171.7725 Evaluate side-chains 387 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 340 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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 c residue 107 LEU Chi-restraints excluded: chain d residue 885 ILE Chi-restraints excluded: chain d residue 915 GLU 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 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 e residue 788 ARG 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 f residue 76 LYS 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 j residue 123 LEU Chi-restraints excluded: chain j residue 215 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 135 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 148 optimal weight: 0.0980 chunk 52 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 328 GLN ** e 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 76 GLN j 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.155725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100175 restraints weight = 18283.340| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.90 r_work: 0.3111 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13572 Z= 0.129 Angle : 0.654 15.177 18324 Z= 0.321 Chirality : 0.044 0.289 2030 Planarity : 0.004 0.045 2364 Dihedral : 4.444 28.379 1807 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.21), residues: 1622 helix: 1.40 (0.20), residues: 723 sheet: -1.02 (0.37), residues: 196 loop : -1.50 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP e 330 HIS 0.004 0.001 HIS e 256 PHE 0.032 0.001 PHE e 267 TYR 0.032 0.001 TYR P 322 ARG 0.014 0.001 ARG d 963 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 550) hydrogen bonds : angle 4.04789 ( 1617) covalent geometry : bond 0.00308 (13572) covalent geometry : angle 0.65396 (18324) *********************** 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 388 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 1.672 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: 0.5425 (tpp) cc_final: 0.5143 (tpt) REVERT: P 219 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.6639 (tmm) REVERT: P 231 ARG cc_start: 0.9241 (ptp-110) cc_final: 0.8803 (ptt-90) REVERT: P 269 ARG cc_start: 0.7518 (mtm180) cc_final: 0.7210 (mtm-85) REVERT: P 271 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8169 (mm-30) REVERT: P 312 LEU cc_start: 0.8091 (pt) cc_final: 0.7673 (mp) REVERT: c 19 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7259 (tp40) REVERT: c 105 ASN cc_start: 0.8780 (m-40) cc_final: 0.8490 (m110) REVERT: d 851 ARG cc_start: 0.8272 (ptm160) cc_final: 0.8029 (ptm-80) REVERT: d 868 LYS cc_start: 0.8736 (ptmm) cc_final: 0.8493 (ptmm) REVERT: d 915 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.8028 (pt0) REVERT: d 931 ASP cc_start: 0.8283 (t0) cc_final: 0.7896 (t0) REVERT: d 932 ASP cc_start: 0.8863 (t70) cc_final: 0.8602 (t0) REVERT: d 958 LYS cc_start: 0.9278 (tppt) cc_final: 0.8848 (tppp) REVERT: e 216 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7681 (pt0) REVERT: e 235 GLU cc_start: 0.9168 (tt0) cc_final: 0.8795 (tt0) REVERT: e 280 ARG cc_start: 0.8837 (ttp80) cc_final: 0.8614 (tmm160) REVERT: e 319 ARG cc_start: 0.8710 (ptp-110) cc_final: 0.8384 (ptp90) REVERT: e 425 ASN cc_start: 0.9200 (t0) cc_final: 0.8713 (t0) REVERT: e 444 MET cc_start: 0.7964 (tmm) cc_final: 0.7708 (tmm) REVERT: e 515 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9029 (mm) REVERT: e 526 ARG cc_start: 0.8358 (tpp80) cc_final: 0.7978 (tpp80) REVERT: e 554 ASP cc_start: 0.8279 (p0) cc_final: 0.7860 (p0) REVERT: e 634 ARG cc_start: 0.8762 (mmt-90) cc_final: 0.8521 (tpp-160) REVERT: e 774 MET cc_start: 0.8827 (mmm) cc_final: 0.8490 (mmm) REVERT: e 788 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7415 (mtt180) REVERT: f 17 GLU cc_start: 0.8258 (mp0) cc_final: 0.7920 (mp0) REVERT: f 65 LYS cc_start: 0.7782 (tptt) cc_final: 0.7318 (tppt) REVERT: f 103 GLU cc_start: 0.8368 (tt0) cc_final: 0.7958 (mp0) REVERT: i 14 LYS cc_start: 0.8487 (tttm) cc_final: 0.8170 (tppt) REVERT: i 21 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7716 (tp40) REVERT: i 97 ARG cc_start: 0.8390 (ttm110) cc_final: 0.8125 (ttp80) REVERT: j 124 GLU cc_start: 0.9064 (tp30) cc_final: 0.8754 (tp30) REVERT: j 165 ASP cc_start: 0.8022 (m-30) cc_final: 0.7793 (m-30) REVERT: j 175 LYS cc_start: 0.8741 (mttt) cc_final: 0.8438 (mttm) REVERT: k 117 GLN cc_start: 0.8301 (pt0) cc_final: 0.7893 (pp30) REVERT: k 122 GLU cc_start: 0.8736 (tt0) cc_final: 0.8410 (tp30) REVERT: k 167 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8147 (tp30) REVERT: k 168 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8063 (tm-30) REVERT: k 193 ARG cc_start: 0.8672 (ttm-80) cc_final: 0.8445 (ttm-80) REVERT: k 199 GLN cc_start: 0.8598 (mm110) cc_final: 0.8375 (mm-40) REVERT: l 64 GLN cc_start: 0.8076 (tp40) cc_final: 0.7795 (tp40) REVERT: l 150 GLN cc_start: 0.8834 (tt0) cc_final: 0.8286 (tt0) REVERT: m 46 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6682 (t0) REVERT: m 80 ARG cc_start: 0.7853 (mmm-85) cc_final: 0.7496 (mmm-85) outliers start: 53 outliers final: 38 residues processed: 360 average time/residue: 0.3396 time to fit residues: 162.0642 Evaluate side-chains 371 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 326 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 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 915 GLU 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 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 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 e residue 788 ARG Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 26 MET Chi-restraints excluded: chain f residue 76 LYS 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 173 CYS Chi-restraints excluded: chain l residue 109 SER Chi-restraints excluded: chain l residue 144 THR Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 46 ASP Chi-restraints excluded: chain m residue 81 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 111 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 71 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 636 HIS ** 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 = 0.3981 r_free = 0.3981 target = 0.154922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099221 restraints weight = 18222.210| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.90 r_work: 0.3097 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13572 Z= 0.147 Angle : 0.660 15.291 18324 Z= 0.326 Chirality : 0.044 0.281 2030 Planarity : 0.005 0.094 2364 Dihedral : 4.440 28.509 1807 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.27 % Allowed : 22.33 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.21), residues: 1622 helix: 1.42 (0.20), residues: 723 sheet: -0.96 (0.37), residues: 196 loop : -1.49 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP e 612 HIS 0.004 0.001 HIS e 256 PHE 0.023 0.001 PHE e 267 TYR 0.016 0.001 TYR i 120 ARG 0.012 0.001 ARG P 318 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 550) hydrogen bonds : angle 4.08103 ( 1617) covalent geometry : bond 0.00353 (13572) covalent geometry : angle 0.66044 (18324) *********************** 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 382 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 334 time to evaluate : 1.507 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: 0.5636 (tpp) cc_final: 0.5317 (tpt) REVERT: P 219 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.6677 (tmm) REVERT: P 231 ARG cc_start: 0.9201 (ptp-110) cc_final: 0.8884 (ptp90) REVERT: P 269 ARG cc_start: 0.7526 (mtm180) cc_final: 0.7181 (mtm-85) REVERT: P 299 ARG cc_start: 0.9304 (mmp80) cc_final: 0.9030 (mmp80) REVERT: P 312 LEU cc_start: 0.8162 (pt) cc_final: 0.7752 (mp) REVERT: c 19 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.7324 (tp40) REVERT: c 27 GLN cc_start: 0.8558 (tt0) cc_final: 0.8222 (tt0) REVERT: c 51 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7825 (mtt180) REVERT: c 105 ASN cc_start: 0.8784 (m-40) cc_final: 0.8481 (m110) REVERT: d 868 LYS cc_start: 0.8747 (ptmm) cc_final: 0.8502 (ptmm) REVERT: d 915 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8041 (pt0) REVERT: d 931 ASP cc_start: 0.8302 (t0) cc_final: 0.7900 (t0) REVERT: d 932 ASP cc_start: 0.8876 (t70) cc_final: 0.8618 (t0) REVERT: e 216 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7536 (pt0) REVERT: e 235 GLU cc_start: 0.9133 (tt0) cc_final: 0.8818 (tt0) REVERT: e 280 ARG cc_start: 0.8879 (ttp80) cc_final: 0.8649 (tmm160) REVERT: e 318 LYS cc_start: 0.8426 (tttt) cc_final: 0.8042 (tmtt) REVERT: e 319 ARG cc_start: 0.8728 (ptp-110) cc_final: 0.8421 (ptp90) REVERT: e 425 ASN cc_start: 0.9219 (t0) cc_final: 0.8724 (t0) REVERT: e 444 MET cc_start: 0.7999 (tmm) cc_final: 0.7736 (tmm) REVERT: e 526 ARG cc_start: 0.8354 (tpp80) cc_final: 0.7974 (tpp80) REVERT: e 634 ARG cc_start: 0.8767 (mmt-90) cc_final: 0.8507 (tpp-160) REVERT: e 774 MET cc_start: 0.8821 (mmm) cc_final: 0.8474 (mmm) REVERT: e 788 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7419 (mtt180) REVERT: f 17 GLU cc_start: 0.8270 (mp0) cc_final: 0.7942 (mp0) REVERT: f 65 LYS cc_start: 0.7818 (tptt) cc_final: 0.7299 (tppt) REVERT: f 103 GLU cc_start: 0.8374 (tt0) cc_final: 0.7970 (mp0) REVERT: i 14 LYS cc_start: 0.8553 (tttm) cc_final: 0.8224 (tppt) REVERT: i 21 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7720 (tp40) REVERT: i 97 ARG cc_start: 0.8385 (ttm110) cc_final: 0.8123 (ttp80) REVERT: j 118 ASP cc_start: 0.8978 (m-30) cc_final: 0.8696 (p0) REVERT: j 124 GLU cc_start: 0.9078 (tp30) cc_final: 0.8785 (tp30) REVERT: j 145 GLU cc_start: 0.7731 (tp30) cc_final: 0.7451 (pm20) REVERT: j 165 ASP cc_start: 0.8032 (m-30) cc_final: 0.7803 (m-30) REVERT: j 175 LYS cc_start: 0.8729 (mttt) cc_final: 0.8441 (mttm) REVERT: k 117 GLN cc_start: 0.8330 (pt0) cc_final: 0.7913 (pp30) REVERT: k 122 GLU cc_start: 0.8748 (tt0) cc_final: 0.8377 (tp30) REVERT: k 123 MET cc_start: 0.9163 (mmt) cc_final: 0.8792 (mmt) REVERT: k 167 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8194 (tp30) REVERT: k 168 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8064 (tm-30) REVERT: k 199 GLN cc_start: 0.8631 (mm110) cc_final: 0.8421 (mm-40) REVERT: l 64 GLN cc_start: 0.8070 (tp40) cc_final: 0.7789 (tp40) REVERT: m 46 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6665 (t0) REVERT: m 80 ARG cc_start: 0.7830 (mmm-85) cc_final: 0.7484 (mmm-85) outliers start: 48 outliers final: 40 residues processed: 358 average time/residue: 0.3497 time to fit residues: 165.9934 Evaluate side-chains 372 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 326 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 286 GLU Chi-restraints excluded: chain P residue 292 ILE 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 915 GLU 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 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 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 e residue 788 ARG Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 26 MET 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 144 THR 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 31 LEU 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 73 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 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 = 0.3979 r_free = 0.3979 target = 0.154597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.098918 restraints weight = 18255.578| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.90 r_work: 0.3093 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4481 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= 0.159 Angle : 0.693 15.511 18324 Z= 0.341 Chirality : 0.045 0.265 2030 Planarity : 0.004 0.044 2364 Dihedral : 4.440 28.558 1807 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.54 % Allowed : 22.46 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1622 helix: 1.39 (0.20), residues: 726 sheet: -0.93 (0.36), residues: 197 loop : -1.49 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP e 612 HIS 0.005 0.001 HIS e 256 PHE 0.028 0.001 PHE m 97 TYR 0.016 0.001 TYR i 120 ARG 0.010 0.001 ARG f 124 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 550) hydrogen bonds : angle 4.09514 ( 1617) covalent geometry : bond 0.00386 (13572) covalent geometry : angle 0.69270 (18324) ********************** 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 382 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 330 time to evaluate : 1.456 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: P 202 MET cc_start: 0.5539 (tpp) cc_final: 0.5204 (tpt) REVERT: P 219 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.6656 (tmm) REVERT: P 231 ARG cc_start: 0.9199 (ptp-110) cc_final: 0.8881 (ptp90) REVERT: P 269 ARG cc_start: 0.7483 (mtm180) cc_final: 0.7098 (mtm-85) REVERT: P 271 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8053 (mm-30) REVERT: P 299 ARG cc_start: 0.9328 (mmp80) cc_final: 0.9035 (mmp80) REVERT: P 312 LEU cc_start: 0.8163 (pt) cc_final: 0.7739 (mp) REVERT: c 19 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.7336 (tp40) REVERT: c 27 GLN cc_start: 0.8559 (tt0) cc_final: 0.8222 (tt0) REVERT: c 51 ARG cc_start: 0.8124 (mtt180) cc_final: 0.7842 (mtt180) REVERT: c 105 ASN cc_start: 0.8803 (m-40) cc_final: 0.8495 (m110) REVERT: d 851 ARG cc_start: 0.8240 (ptm160) cc_final: 0.7933 (ptm160) REVERT: d 868 LYS cc_start: 0.8703 (ptmm) cc_final: 0.8456 (ptmm) REVERT: d 915 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8052 (pt0) REVERT: d 931 ASP cc_start: 0.8310 (t0) cc_final: 0.7906 (t0) REVERT: d 932 ASP cc_start: 0.8866 (t70) cc_final: 0.8556 (t70) REVERT: d 958 LYS cc_start: 0.9272 (tppt) cc_final: 0.8978 (tppp) REVERT: d 963 ARG cc_start: 0.8898 (ptt-90) cc_final: 0.8643 (ptt-90) REVERT: e 216 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7590 (pt0) REVERT: e 235 GLU cc_start: 0.9133 (tt0) cc_final: 0.8804 (tt0) REVERT: e 280 ARG cc_start: 0.8892 (ttp80) cc_final: 0.8662 (tmm160) REVERT: e 318 LYS cc_start: 0.8445 (tttt) cc_final: 0.8068 (tmtt) REVERT: e 319 ARG cc_start: 0.8734 (ptp-110) cc_final: 0.8412 (ptp90) REVERT: e 425 ASN cc_start: 0.9212 (t0) cc_final: 0.8721 (t0) REVERT: e 444 MET cc_start: 0.8015 (tmm) cc_final: 0.7756 (tmm) REVERT: e 480 ASP cc_start: 0.8432 (t0) cc_final: 0.8227 (t0) REVERT: e 515 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9127 (mm) REVERT: e 526 ARG cc_start: 0.8487 (tpp80) cc_final: 0.8091 (tpp80) REVERT: e 634 ARG cc_start: 0.8763 (mmt-90) cc_final: 0.8499 (tpp-160) REVERT: e 774 MET cc_start: 0.8831 (mmm) cc_final: 0.8486 (mmm) REVERT: e 788 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7416 (mtt-85) REVERT: f 17 GLU cc_start: 0.8255 (mp0) cc_final: 0.7923 (mp0) REVERT: f 65 LYS cc_start: 0.7830 (tptt) cc_final: 0.7364 (tppt) REVERT: f 103 GLU cc_start: 0.8389 (tt0) cc_final: 0.8003 (mp0) REVERT: i 14 LYS cc_start: 0.8570 (tttm) cc_final: 0.8243 (tppt) REVERT: i 21 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7733 (tp40) REVERT: i 97 ARG cc_start: 0.8411 (ttm110) cc_final: 0.8097 (ttp80) REVERT: j 124 GLU cc_start: 0.9076 (tp30) cc_final: 0.8676 (tp30) REVERT: j 145 GLU cc_start: 0.7722 (tp30) cc_final: 0.7441 (pm20) REVERT: j 165 ASP cc_start: 0.8028 (m-30) cc_final: 0.7797 (m-30) REVERT: j 175 LYS cc_start: 0.8723 (mttt) cc_final: 0.8442 (mttm) REVERT: k 117 GLN cc_start: 0.8395 (pt0) cc_final: 0.7955 (pp30) REVERT: k 122 GLU cc_start: 0.8768 (tt0) cc_final: 0.8331 (tp30) REVERT: k 123 MET cc_start: 0.9127 (mmt) cc_final: 0.8759 (mmt) REVERT: k 167 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8194 (tp30) REVERT: k 168 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8148 (tm-30) REVERT: k 199 GLN cc_start: 0.8643 (mm110) cc_final: 0.8434 (mm-40) REVERT: l 64 GLN cc_start: 0.8110 (tp40) cc_final: 0.7819 (tp40) REVERT: l 150 GLN cc_start: 0.8814 (tt0) cc_final: 0.8340 (tt0) REVERT: m 46 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6617 (t0) REVERT: m 80 ARG cc_start: 0.7863 (mmm-85) cc_final: 0.7527 (mmm-85) outliers start: 52 outliers final: 42 residues processed: 354 average time/residue: 0.3511 time to fit residues: 165.0477 Evaluate side-chains 377 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 328 time to evaluate : 1.658 ------------------------------------------------------------------------------- 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 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 915 GLU 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 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 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 e residue 788 ARG Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 26 MET 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 109 SER Chi-restraints excluded: chain m residue 31 LEU Chi-restraints excluded: chain m residue 46 ASP Chi-restraints excluded: chain m residue 81 VAL Chi-restraints excluded: chain m residue 102 ASP 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: 1.9990 chunk 87 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 chunk 74 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 11 optimal weight: 0.0050 chunk 53 optimal weight: 6.9990 chunk 68 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 268 HIS ** e 636 HIS ** 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 = 0.3997 r_free = 0.3997 target = 0.156175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.100823 restraints weight = 18217.940| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.91 r_work: 0.3121 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13572 Z= 0.126 Angle : 0.669 15.521 18324 Z= 0.329 Chirality : 0.044 0.256 2030 Planarity : 0.004 0.064 2364 Dihedral : 4.334 28.036 1807 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.13 % Allowed : 22.40 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1622 helix: 1.50 (0.20), residues: 726 sheet: -0.81 (0.37), residues: 195 loop : -1.52 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP e 330 HIS 0.004 0.001 HIS e 256 PHE 0.020 0.001 PHE e 267 TYR 0.020 0.001 TYR P 283 ARG 0.010 0.001 ARG f 124 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 550) hydrogen bonds : angle 4.01250 ( 1617) covalent geometry : bond 0.00300 (13572) covalent geometry : angle 0.66883 (18324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8613.48 seconds wall clock time: 153 minutes 59.85 seconds (9239.85 seconds total)