Starting phenix.real_space_refine on Mon Jul 6 07:17:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8abe_15318/07_2026/8abe_15318.cif Found real_map, /net/cci-nas-00/data/ceres_data/8abe_15318/07_2026/8abe_15318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8abe_15318/07_2026/8abe_15318.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8abe_15318/07_2026/8abe_15318.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8abe_15318/07_2026/8abe_15318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8abe_15318/07_2026/8abe_15318.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8abe_15318/07_2026/8abe_15318.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8abe_15318/07_2026/8abe_15318.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 21031 2.51 5 N 5296 2.21 5 O 6073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 125 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32540 Number of models: 1 Model: "" Number of chains: 32 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "M" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "O" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "S" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "C" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'FES': 1, 'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "N" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "E" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 30.092 49.960 34.487 1.00 85.40 S ATOM 4207 SG CYS P 187 32.630 47.255 33.484 1.00 99.81 S Time building chain proxies: 6.13, per 1000 atoms: 0.19 Number of scatterers: 32540 At special positions: 0 Unit cell: (119.691, 129.735, 164.889, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 8 26.01 S 102 16.00 P 30 15.00 O 6073 8.00 N 5296 7.00 C 21031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.06 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.07 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.06 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " Number of angles added : 3 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7486 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 21 sheets defined 61.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 7 through 18 Processing helix chain 'C' and resid 27 through 30 Processing helix chain 'C' and resid 31 through 52 Processing helix chain 'C' and resid 60 through 71 Processing helix chain 'C' and resid 74 through 103 removed outlier: 3.781A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 134 removed outlier: 3.538A pdb=" N LEU C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 149 Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 172 through 202 Proline residue: C 187 - end of helix Processing helix chain 'C' and resid 221 through 247 removed outlier: 6.896A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 275 through 285 removed outlier: 3.774A pdb=" N ILE C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.806A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 Processing helix chain 'C' and resid 319 through 340 Processing helix chain 'C' and resid 347 through 365 removed outlier: 4.122A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 383 Processing helix chain 'P' and resid 58 through 89 removed outlier: 3.610A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 92 No H-bonds generated for 'chain 'P' and resid 90 through 92' Processing helix chain 'P' and resid 94 through 99 Processing helix chain 'P' and resid 131 through 139 Processing helix chain 'P' and resid 151 through 156 Processing helix chain 'G' and resid 3 through 17 Processing helix chain 'G' and resid 17 through 36 Proline residue: G 26 - end of helix removed outlier: 3.529A pdb=" N GLY G 36 " --> pdb=" O VAL G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 41 Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 52 through 61 Processing helix chain 'G' and resid 63 through 84 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 94 through 98 Processing helix chain 'G' and resid 102 through 120 Processing helix chain 'F' and resid 77 through 89 removed outlier: 4.323A pdb=" N ALA F 81 " --> pdb=" O ASP F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 111 Processing helix chain 'F' and resid 123 through 137 Processing helix chain 'F' and resid 138 through 145 removed outlier: 3.595A pdb=" N VAL F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 71 through 80 removed outlier: 3.527A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 122 through 136 Processing helix chain 'A' and resid 140 through 155 removed outlier: 4.032A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 5.020A pdb=" N ASN A 159 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 160 " --> pdb=" O GLU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 160' Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 311 through 317 removed outlier: 4.011A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 328 Processing helix chain 'A' and resid 358 through 376 removed outlier: 3.607A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.554A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 419 through 429 Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.659A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 69 through 80 Processing helix chain 'B' and resid 103 through 118 removed outlier: 3.596A pdb=" N PHE B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.603A pdb=" N THR B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.821A pdb=" N ALA B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 310 through 331 Processing helix chain 'B' and resid 333 through 354 Processing helix chain 'B' and resid 354 through 368 removed outlier: 3.679A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.599A pdb=" N VAL B 378 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 395 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 109 through 123 Processing helix chain 'D' and resid 124 through 127 Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 144 through 154 Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 266 through 283 Processing helix chain 'D' and resid 285 through 320 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 39 through 81 removed outlier: 4.390A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix Processing helix chain 'H' and resid 85 through 93 Processing helix chain 'I' and resid 5 through 12 Processing helix chain 'I' and resid 14 through 45 Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.543A pdb=" N ILE I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 57 No H-bonds generated for 'chain 'I' and resid 55 through 57' Processing helix chain 'J' and resid 25 through 50 removed outlier: 3.547A pdb=" N TRP J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) Proline residue: J 33 - end of helix Processing helix chain 'J' and resid 53 through 60 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 66 through 72 removed outlier: 3.773A pdb=" N GLU J 69 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.664A pdb=" N ASN J 80 " --> pdb=" O ALA J 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 7 through 18 Processing helix chain 'N' and resid 27 through 30 Processing helix chain 'N' and resid 31 through 52 Processing helix chain 'N' and resid 60 through 71 Processing helix chain 'N' and resid 74 through 103 removed outlier: 3.790A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 134 removed outlier: 3.558A pdb=" N LEU N 134 " --> pdb=" O MET N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 149 Processing helix chain 'N' and resid 150 through 154 Processing helix chain 'N' and resid 157 through 167 Processing helix chain 'N' and resid 172 through 202 Proline residue: N 187 - end of helix Processing helix chain 'N' and resid 221 through 247 removed outlier: 6.902A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR N 232 " --> pdb=" O LYS N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 258 Processing helix chain 'N' and resid 272 through 274 No H-bonds generated for 'chain 'N' and resid 272 through 274' Processing helix chain 'N' and resid 275 through 285 removed outlier: 3.789A pdb=" N ILE N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 301 removed outlier: 3.802A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 309 Processing helix chain 'N' and resid 319 through 340 Processing helix chain 'N' and resid 347 through 365 removed outlier: 4.133A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 383 Processing helix chain 'E' and resid 58 through 89 removed outlier: 3.628A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 92 No H-bonds generated for 'chain 'E' and resid 90 through 92' Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'R' and resid 3 through 17 Processing helix chain 'R' and resid 17 through 36 Proline residue: R 26 - end of helix removed outlier: 3.515A pdb=" N GLY R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 41 Processing helix chain 'R' and resid 43 through 48 Processing helix chain 'R' and resid 52 through 61 Processing helix chain 'R' and resid 63 through 84 Processing helix chain 'R' and resid 88 through 92 Processing helix chain 'R' and resid 94 through 98 Processing helix chain 'R' and resid 102 through 120 Processing helix chain 'Q' and resid 77 through 89 removed outlier: 4.259A pdb=" N ALA Q 81 " --> pdb=" O ASP Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 111 Processing helix chain 'Q' and resid 123 through 137 Processing helix chain 'Q' and resid 138 through 145 removed outlier: 3.598A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 Processing helix chain 'L' and resid 71 through 78 removed outlier: 3.504A pdb=" N HIS L 78 " --> pdb=" O HIS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 100 Processing helix chain 'L' and resid 122 through 136 Processing helix chain 'L' and resid 140 through 155 removed outlier: 4.033A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 160 removed outlier: 5.016A pdb=" N ASN L 159 " --> pdb=" O GLU L 156 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS L 160 " --> pdb=" O GLU L 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 156 through 160' Processing helix chain 'L' and resid 161 through 175 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 187 through 192 Processing helix chain 'L' and resid 195 through 207 Processing helix chain 'L' and resid 208 through 210 No H-bonds generated for 'chain 'L' and resid 208 through 210' Processing helix chain 'L' and resid 221 through 233 Processing helix chain 'L' and resid 293 through 305 Processing helix chain 'L' and resid 311 through 317 removed outlier: 3.997A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 328 Processing helix chain 'L' and resid 358 through 376 removed outlier: 3.624A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 378 through 396 removed outlier: 3.683A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU L 394 " --> pdb=" O LYS L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 399 through 414 Processing helix chain 'L' and resid 419 through 429 Processing helix chain 'L' and resid 431 through 443 Processing helix chain 'L' and resid 461 through 468 removed outlier: 3.665A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 48 Processing helix chain 'M' and resid 52 through 60 Processing helix chain 'M' and resid 69 through 80 Processing helix chain 'M' and resid 103 through 118 removed outlier: 3.578A pdb=" N PHE M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR M 118 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 128 through 142 Processing helix chain 'M' and resid 143 through 158 removed outlier: 3.591A pdb=" N THR M 147 " --> pdb=" O ASP M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 163 Processing helix chain 'M' and resid 174 through 186 Processing helix chain 'M' and resid 187 through 189 No H-bonds generated for 'chain 'M' and resid 187 through 189' Processing helix chain 'M' and resid 199 through 211 Processing helix chain 'M' and resid 254 through 264 removed outlier: 3.818A pdb=" N ALA M 258 " --> pdb=" O PRO M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.774A pdb=" N VAL M 283 " --> pdb=" O GLN M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 331 Processing helix chain 'M' and resid 333 through 354 Processing helix chain 'M' and resid 354 through 367 removed outlier: 3.923A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 378 removed outlier: 3.565A pdb=" N VAL M 378 " --> pdb=" O PRO M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 395 Processing helix chain 'M' and resid 406 through 410 Processing helix chain 'M' and resid 412 through 416 Processing helix chain 'O' and resid 86 through 91 Processing helix chain 'O' and resid 109 through 123 Processing helix chain 'O' and resid 124 through 127 Processing helix chain 'O' and resid 134 through 139 Processing helix chain 'O' and resid 144 through 154 Processing helix chain 'O' and resid 184 through 191 Processing helix chain 'O' and resid 210 through 220 Processing helix chain 'O' and resid 266 through 283 Processing helix chain 'O' and resid 285 through 320 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 39 through 81 removed outlier: 4.390A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix Processing helix chain 'S' and resid 85 through 93 Processing helix chain 'T' and resid 5 through 12 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'T' and resid 49 through 54 removed outlier: 3.545A pdb=" N ILE T 53 " --> pdb=" O GLN T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 57 No H-bonds generated for 'chain 'T' and resid 55 through 57' Processing helix chain 'U' and resid 25 through 50 removed outlier: 3.556A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP U 31 " --> pdb=" O THR U 27 " (cutoff:3.500A) Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 53 through 60 Processing helix chain 'U' and resid 61 through 64 Processing helix chain 'U' and resid 66 through 72 removed outlier: 3.777A pdb=" N GLU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 80 removed outlier: 3.658A pdb=" N ASN U 80 " --> pdb=" O ALA U 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'P' and resid 103 through 106 Processing sheet with id=AA3, first strand: chain 'P' and resid 114 through 120 removed outlier: 3.890A pdb=" N LYS P 114 " --> pdb=" O HIS P 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 176 through 177 removed outlier: 3.602A pdb=" N ARG P 202 " --> pdb=" O HIS P 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 122 through 124 Processing sheet with id=AA6, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.534A pdb=" N THR A 40 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLY A 216 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA A 42 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLY A 218 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU A 44 " --> pdb=" O GLY A 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 306 through 308 removed outlier: 3.987A pdb=" N ARG A 271 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE H 24 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 16 through 20 removed outlier: 4.184A pdb=" N LYS B 24 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.593A pdb=" N GLY B 231 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ALA B 403 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA B 233 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN B 241 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 156 through 158 Processing sheet with id=AB2, first strand: chain 'D' and resid 236 through 237 Processing sheet with id=AB3, first strand: chain 'J' and resid 14 through 16 Processing sheet with id=AB4, first strand: chain 'J' and resid 19 through 20 Processing sheet with id=AB5, first strand: chain 'N' and resid 21 through 23 Processing sheet with id=AB6, first strand: chain 'L' and resid 31 through 34 removed outlier: 6.545A pdb=" N THR L 40 " --> pdb=" O LEU L 214 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLY L 216 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA L 42 " --> pdb=" O GLY L 216 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N GLY L 218 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU L 44 " --> pdb=" O GLY L 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 307 through 308 removed outlier: 3.927A pdb=" N ARG L 271 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE S 24 " --> pdb=" O ARG L 271 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 16 through 20 removed outlier: 4.206A pdb=" N LYS M 24 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 231 through 235 removed outlier: 6.564A pdb=" N GLY M 231 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ALA M 403 " --> pdb=" O GLY M 231 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA M 233 " --> pdb=" O ALA M 403 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN M 241 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 156 through 158 Processing sheet with id=AC2, first strand: chain 'O' and resid 236 through 237 Processing sheet with id=AC3, first strand: chain 'U' and resid 19 through 20 1895 hydrogen bonds defined for protein. 5328 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: 5.87 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.40: 13564 1.40 - 1.61: 19597 1.61 - 1.82: 167 1.82 - 2.03: 19 2.03 - 2.24: 20 Bond restraints: 33367 Sorted by residual: bond pdb=" C18 XP4 L3003 " pdb=" O7 XP4 L3003 " ideal model delta sigma weight residual 1.328 1.464 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C18 XP4 A3003 " pdb=" O7 XP4 A3003 " ideal model delta sigma weight residual 1.328 1.459 -0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" C2C HEC O 401 " pdb=" C3C HEC O 401 " ideal model delta sigma weight residual 1.334 1.461 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C2C HEC D 401 " pdb=" C3C HEC D 401 " ideal model delta sigma weight residual 1.334 1.458 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C2B HEC O 401 " pdb=" C3B HEC O 401 " ideal model delta sigma weight residual 1.334 1.455 -0.121 2.00e-02 2.50e+03 3.67e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 43847 4.02 - 8.04: 1341 8.04 - 12.06: 130 12.06 - 16.08: 29 16.08 - 20.10: 5 Bond angle restraints: 45352 Sorted by residual: angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 95.28 15.99 1.47e+00 4.63e-01 1.18e+02 angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 95.77 15.50 1.47e+00 4.63e-01 1.11e+02 angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 93.19 11.14 1.14e+00 7.69e-01 9.55e+01 angle pdb=" C GLN B 215 " pdb=" CA GLN B 215 " pdb=" CB GLN B 215 " ideal model delta sigma weight residual 109.64 92.54 17.10 1.77e+00 3.19e-01 9.33e+01 angle pdb=" C GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta sigma weight residual 109.64 92.58 17.06 1.77e+00 3.19e-01 9.29e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.41: 18513 31.41 - 62.82: 907 62.82 - 94.22: 93 94.22 - 125.63: 1 125.63 - 157.04: 1 Dihedral angle restraints: 19515 sinusoidal: 7896 harmonic: 11619 Sorted by residual: dihedral pdb=" C GLN M 215 " pdb=" N GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta harmonic sigma weight residual -122.60 -101.65 -20.95 0 2.50e+00 1.60e-01 7.02e+01 dihedral pdb=" C GLN B 215 " pdb=" N GLN B 215 " pdb=" CA GLN B 215 " pdb=" CB GLN B 215 " ideal model delta harmonic sigma weight residual -122.60 -101.67 -20.93 0 2.50e+00 1.60e-01 7.01e+01 dihedral pdb=" C GLU O 283 " pdb=" N GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta harmonic sigma weight residual -122.60 -103.30 -19.30 0 2.50e+00 1.60e-01 5.96e+01 ... (remaining 19512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 4340 0.167 - 0.334: 575 0.334 - 0.501: 40 0.501 - 0.669: 3 0.669 - 0.836: 4 Chirality restraints: 4962 Sorted by residual: chirality pdb=" CB4 CDL N 505 " pdb=" CB3 CDL N 505 " pdb=" CB6 CDL N 505 " pdb=" OB6 CDL N 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.74 -0.84 2.00e-01 2.50e+01 1.75e+01 chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.77 -0.81 2.00e-01 2.50e+01 1.63e+01 chirality pdb=" CB4 CDL S 702 " pdb=" CB3 CDL S 702 " pdb=" CB6 CDL S 702 " pdb=" OB6 CDL S 702 " both_signs ideal model delta sigma weight residual False -2.57 -1.80 -0.77 2.00e-01 2.50e+01 1.49e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS L 78 " 0.025 2.00e-02 2.50e+03 5.22e-02 2.73e+01 pdb=" C HIS L 78 " -0.090 2.00e-02 2.50e+03 pdb=" O HIS L 78 " 0.034 2.00e-02 2.50e+03 pdb=" N LEU L 79 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS N 96 " -0.052 2.00e-02 2.50e+03 3.99e-02 2.38e+01 pdb=" CG HIS N 96 " 0.069 2.00e-02 2.50e+03 pdb=" ND1 HIS N 96 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS N 96 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 HIS N 96 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 HIS N 96 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEM N 502 " 0.009 2.00e-02 2.50e+03 2.99e-02 2.02e+01 pdb=" C2C HEM N 502 " 0.029 2.00e-02 2.50e+03 pdb=" C3C HEM N 502 " 0.006 2.00e-02 2.50e+03 pdb=" C4C HEM N 502 " 0.038 2.00e-02 2.50e+03 pdb=" CAC HEM N 502 " -0.035 2.00e-02 2.50e+03 pdb=" CHC HEM N 502 " -0.054 2.00e-02 2.50e+03 pdb=" CHD HEM N 502 " -0.029 2.00e-02 2.50e+03 pdb=" CMC HEM N 502 " 0.011 2.00e-02 2.50e+03 pdb=" NC HEM N 502 " 0.025 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 227 2.62 - 3.19: 28276 3.19 - 3.76: 53556 3.76 - 4.33: 78848 4.33 - 4.90: 122061 Nonbonded interactions: 282968 Sorted by model distance: nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.050 3.120 nonbonded pdb=" NE2 HIS C 183 " pdb="FE HEM C 501 " model vdw 2.061 3.080 nonbonded pdb=" NE2 HIS N 82 " pdb="FE HEM N 501 " model vdw 2.066 3.080 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.155 3.080 nonbonded pdb=" SD MET O 248 " pdb="FE HEC O 401 " model vdw 2.231 3.360 ... (remaining 282963 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'U' } 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: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 33.020 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.110 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9505 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 : 0.011 0.476 33383 Z= 0.685 Angle : 1.726 20.096 45365 Z= 1.066 Chirality : 0.113 0.836 4962 Planarity : 0.008 0.146 5700 Dihedral : 17.448 157.039 12014 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.37 % Allowed : 6.77 % Favored : 89.86 % Cbeta Deviations : 0.99 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.12), residues: 3955 helix: -0.82 (0.09), residues: 2142 sheet: 0.17 (0.25), residues: 351 loop : -0.65 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.046 0.003 ARG G 76 TYR 0.055 0.008 TYR O 259 PHE 0.059 0.007 PHE B 107 TRP 0.048 0.009 TRP O 280 HIS 0.019 0.005 HIS L 279 Details of bonding type rmsd/Z covalent geometry : bond 0.01030 / 0.63 (33367) covalent geometry : angle 1.72343 / 1.07 (45352) SS BOND : bond 0.02983 / 1.67 ( 5) SS BOND : angle 2.52423 / 1.31 ( 10) hydrogen bonds : bond 0.18505 / 12.19 ( 1895) hydrogen bonds : angle 6.86906 / 4.99 ( 5328) metal coordination : bond 0.10242 / 5.08 ( 4) metal coordination : angle 10.50342 / 5.75 ( 3) Misc. bond : bond 0.20886 / 8.36 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 461 time to evaluate : 1.256 Fit side-chains REVERT: P 102 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7424 (mppt) REVERT: P 104 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8514 (mp0) REVERT: P 112 LEU cc_start: 0.9236 (mt) cc_final: 0.8996 (tp) REVERT: P 134 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7599 (mt-10) REVERT: P 158 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7273 (tppt) REVERT: P 182 PHE cc_start: 0.8571 (m-80) cc_final: 0.8190 (m-80) REVERT: P 197 SER cc_start: 0.8274 (OUTLIER) cc_final: 0.7815 (t) REVERT: G 9 LYS cc_start: 0.9048 (mttp) cc_final: 0.8731 (tttt) REVERT: F 84 GLU cc_start: 0.8691 (tt0) cc_final: 0.8259 (mt-10) REVERT: F 88 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8225 (mm-30) REVERT: A 97 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: B 205 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8560 (tm-30) REVERT: B 364 MET cc_start: 0.8899 (tpp) cc_final: 0.8692 (tpp) REVERT: D 90 HIS cc_start: 0.9138 (m-70) cc_final: 0.8875 (m-70) REVERT: I 30 ASP cc_start: 0.9152 (t70) cc_final: 0.8880 (t70) REVERT: I 43 ARG cc_start: 0.8721 (mtm110) cc_final: 0.8409 (ttp-110) REVERT: J 73 ARG cc_start: 0.9020 (ptt-90) cc_final: 0.8733 (ptt180) REVERT: N 69 MET cc_start: 0.9450 (mmm) cc_final: 0.9142 (mmm) REVERT: R 33 LYS cc_start: 0.9335 (tttt) cc_final: 0.9120 (ttpp) REVERT: Q 103 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7869 (mt-10) REVERT: L 87 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8538 (mtt90) REVERT: L 390 LYS cc_start: 0.9044 (tptt) cc_final: 0.8828 (mtmt) REVERT: M 16 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8728 (p) REVERT: M 205 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8666 (tm130) REVERT: M 236 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8170 (mtp85) REVERT: M 331 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: U 73 ARG cc_start: 0.8774 (ptt-90) cc_final: 0.8416 (ptt180) outliers start: 112 outliers final: 11 residues processed: 526 average time/residue: 0.8487 time to fit residues: 512.6573 Evaluate side-chains 335 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 316 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 197 SER Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain M residue 331 GLU Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN C 22 GLN C 173 ASN C 202 HIS C 332 ASN P 90 ASN P 115 ASN G 84 HIS F 97 HIS F 109 GLN A 222 HIS A 371 ASN A 379 ASN B 87 HIS B 168 GLN B 197 ASN B 295 ASN B 354 ASN B 377 ASN J 80 ASN N 14 ASN N 202 HIS N 332 ASN E 90 ASN R 84 HIS Q 92 HIS L 332 ASN L 371 ASN M 87 HIS M 377 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.055850 restraints weight = 56423.831| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 1.66 r_work: 0.2572 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9387 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.415 33383 Z= 0.155 Angle : 0.635 14.912 45365 Z= 0.317 Chirality : 0.043 0.173 4962 Planarity : 0.004 0.035 5700 Dihedral : 11.981 128.368 4866 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.62 % Allowed : 10.41 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.13), residues: 3955 helix: 1.11 (0.11), residues: 2156 sheet: 0.52 (0.26), residues: 368 loop : 0.12 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 62 TYR 0.021 0.002 TYR D 237 PHE 0.022 0.002 PHE L 334 TRP 0.030 0.002 TRP C 156 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (33367) covalent geometry : angle 0.63441 / 0.32 (45352) SS BOND : bond 0.00221 / 0.12 ( 5) SS BOND : angle 0.68779 / 0.35 ( 10) hydrogen bonds : bond 0.05301 / 3.50 ( 1895) hydrogen bonds : angle 4.71403 / 3.45 ( 5328) metal coordination : bond 0.01634 / 0.82 ( 4) metal coordination : angle 2.88102 / 1.58 ( 3) Misc. bond : bond 0.27114 / 15.83 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 346 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: G 9 LYS cc_start: 0.8893 (mttp) cc_final: 0.8503 (tttt) REVERT: F 84 GLU cc_start: 0.8707 (tt0) cc_final: 0.8218 (mt-10) REVERT: F 88 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7936 (mm-30) REVERT: F 120 LYS cc_start: 0.9156 (mttp) cc_final: 0.8943 (mmtm) REVERT: F 122 ASP cc_start: 0.8509 (p0) cc_final: 0.8296 (p0) REVERT: A 97 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: A 397 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8057 (mt) REVERT: B 139 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8901 (ttmm) REVERT: B 353 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: B 364 MET cc_start: 0.8837 (tpp) cc_final: 0.8505 (tpp) REVERT: I 30 ASP cc_start: 0.9069 (t70) cc_final: 0.8765 (t70) REVERT: J 15 LYS cc_start: 0.8662 (mtmm) cc_final: 0.8361 (ptpt) REVERT: J 73 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8352 (ptt180) REVERT: J 74 GLU cc_start: 0.7899 (pm20) cc_final: 0.7663 (pp20) REVERT: Q 96 HIS cc_start: 0.8627 (t-170) cc_final: 0.8282 (t70) REVERT: M 251 GLU cc_start: 0.7800 (pm20) cc_final: 0.7591 (pm20) REVERT: M 364 MET cc_start: 0.8661 (tpp) cc_final: 0.8372 (tpp) REVERT: U 73 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8057 (ptt180) outliers start: 54 outliers final: 10 residues processed: 383 average time/residue: 0.8619 time to fit residues: 380.8813 Evaluate side-chains 310 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 294 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 275 optimal weight: 6.9990 chunk 317 optimal weight: 2.9990 chunk 252 optimal weight: 0.8980 chunk 255 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 377 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 384 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 ASN P 85 GLN F 109 GLN B 168 GLN B 377 ASN D 90 HIS I 39 ASN J 58 GLN J 80 ASN L 332 ASN M 197 ASN M 377 ASN M 408 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.071584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.052904 restraints weight = 56965.921| |-----------------------------------------------------------------------------| r_work (start): 0.2619 rms_B_bonded: 1.66 r_work: 0.2511 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2398 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9427 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.377 33383 Z= 0.277 Angle : 0.672 15.132 45365 Z= 0.332 Chirality : 0.046 0.171 4962 Planarity : 0.005 0.048 5700 Dihedral : 11.384 96.709 4823 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.35 % Allowed : 11.31 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.13), residues: 3955 helix: 1.50 (0.11), residues: 2150 sheet: 0.72 (0.26), residues: 360 loop : 0.30 (0.17), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 236 TYR 0.021 0.002 TYR D 117 PHE 0.023 0.002 PHE L 334 TRP 0.022 0.002 TRP C 142 HIS 0.012 0.001 HIS C 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.28 (33367) covalent geometry : angle 0.67067 / 0.33 (45352) SS BOND : bond 0.00377 / 0.20 ( 5) SS BOND : angle 0.66026 / 0.32 ( 10) hydrogen bonds : bond 0.05880 / 3.89 ( 1895) hydrogen bonds : angle 4.61056 / 3.36 ( 5328) metal coordination : bond 0.03220 / 1.61 ( 4) metal coordination : angle 5.53114 / 3.14 ( 3) Misc. bond : bond 0.28170 / 15.84 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 297 time to evaluate : 1.327 Fit side-chains REVERT: G 9 LYS cc_start: 0.8912 (mttp) cc_final: 0.8559 (tttt) REVERT: F 84 GLU cc_start: 0.8656 (tt0) cc_final: 0.8259 (mt-10) REVERT: F 120 LYS cc_start: 0.9132 (mttp) cc_final: 0.8894 (mmtm) REVERT: F 122 ASP cc_start: 0.8639 (p0) cc_final: 0.8408 (p0) REVERT: A 87 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8879 (ptp90) REVERT: A 97 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: A 99 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8486 (ttm) REVERT: A 397 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8069 (mt) REVERT: B 139 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8882 (ttmm) REVERT: B 232 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8535 (mt-10) REVERT: B 251 GLU cc_start: 0.8108 (pm20) cc_final: 0.7893 (pm20) REVERT: B 364 MET cc_start: 0.8870 (tpp) cc_final: 0.8566 (tpp) REVERT: I 30 ASP cc_start: 0.9072 (t70) cc_final: 0.8823 (t70) REVERT: J 15 LYS cc_start: 0.8763 (mtmm) cc_final: 0.8560 (ptpt) REVERT: J 73 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8488 (ptt180) REVERT: R 66 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8573 (mm-30) REVERT: Q 96 HIS cc_start: 0.8745 (t-170) cc_final: 0.8538 (t70) REVERT: Q 110 GLU cc_start: 0.8390 (pt0) cc_final: 0.8066 (pp20) REVERT: M 251 GLU cc_start: 0.7979 (pm20) cc_final: 0.7767 (pm20) REVERT: O 248 MET cc_start: 0.9417 (ttp) cc_final: 0.9189 (ttp) REVERT: U 73 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8035 (ptt180) outliers start: 45 outliers final: 19 residues processed: 323 average time/residue: 0.8182 time to fit residues: 305.3941 Evaluate side-chains 309 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 281 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 364 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 295 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 220 optimal weight: 0.1980 chunk 384 optimal weight: 6.9990 chunk 337 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 HIS P 115 ASN F 109 GLN B 316 GLN B 377 ASN J 58 GLN J 80 ASN M 316 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.055899 restraints weight = 56440.277| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 1.65 r_work: 0.2584 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9385 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.372 33383 Z= 0.124 Angle : 0.541 13.514 45365 Z= 0.265 Chirality : 0.041 0.147 4962 Planarity : 0.004 0.052 5700 Dihedral : 10.622 89.388 4823 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.99 % Allowed : 11.46 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.14), residues: 3955 helix: 1.86 (0.11), residues: 2162 sheet: 0.90 (0.27), residues: 359 loop : 0.55 (0.18), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 236 TYR 0.015 0.001 TYR D 117 PHE 0.020 0.001 PHE L 334 TRP 0.016 0.001 TRP C 142 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (33367) covalent geometry : angle 0.53911 / 0.26 (45352) SS BOND : bond 0.00248 / 0.14 ( 5) SS BOND : angle 0.52514 / 0.26 ( 10) hydrogen bonds : bond 0.04436 / 2.92 ( 1895) hydrogen bonds : angle 4.34749 / 3.17 ( 5328) metal coordination : bond 0.01273 / 0.64 ( 4) metal coordination : angle 5.00295 / 2.74 ( 3) Misc. bond : bond 0.24856 / 14.64 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 306 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 9 LYS cc_start: 0.8890 (mttp) cc_final: 0.8568 (ttpt) REVERT: F 84 GLU cc_start: 0.8682 (tt0) cc_final: 0.8202 (mt-10) REVERT: F 88 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8151 (mm-30) REVERT: F 120 LYS cc_start: 0.9132 (mttp) cc_final: 0.8893 (mmtp) REVERT: F 122 ASP cc_start: 0.8573 (p0) cc_final: 0.8336 (p0) REVERT: A 97 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: B 251 GLU cc_start: 0.8147 (pm20) cc_final: 0.7944 (pm20) REVERT: B 353 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: B 364 MET cc_start: 0.8881 (tpp) cc_final: 0.8578 (tpp) REVERT: D 163 ASP cc_start: 0.8747 (m-30) cc_final: 0.8392 (p0) REVERT: I 30 ASP cc_start: 0.9040 (t70) cc_final: 0.8796 (t70) REVERT: J 15 LYS cc_start: 0.8706 (mtmm) cc_final: 0.8449 (ptpt) REVERT: J 58 GLN cc_start: 0.8613 (mt0) cc_final: 0.8300 (mt0) REVERT: J 73 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8515 (ptt180) REVERT: M 364 MET cc_start: 0.8741 (tpp) cc_final: 0.8301 (tpt) REVERT: U 10 LYS cc_start: 0.9053 (tptp) cc_final: 0.8820 (tptt) REVERT: U 55 ARG cc_start: 0.9083 (ttm110) cc_final: 0.8803 (ttp-170) REVERT: U 73 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8298 (ptp-170) outliers start: 33 outliers final: 11 residues processed: 329 average time/residue: 0.8427 time to fit residues: 320.7097 Evaluate side-chains 300 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 285 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 99 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 287 optimal weight: 4.9990 chunk 275 optimal weight: 0.9990 chunk 294 optimal weight: 2.9990 chunk 369 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 321 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 109 GLN B 377 ASN Q 96 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.074151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.055786 restraints weight = 56478.903| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 1.64 r_work: 0.2583 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9385 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.360 33383 Z= 0.129 Angle : 0.537 14.330 45365 Z= 0.260 Chirality : 0.041 0.144 4962 Planarity : 0.004 0.050 5700 Dihedral : 10.193 89.201 4822 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.23 % Allowed : 11.55 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.14), residues: 3955 helix: 2.02 (0.11), residues: 2174 sheet: 0.99 (0.27), residues: 359 loop : 0.65 (0.18), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 62 TYR 0.017 0.001 TYR C 225 PHE 0.019 0.001 PHE L 334 TRP 0.015 0.001 TRP C 142 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (33367) covalent geometry : angle 0.53536 / 0.26 (45352) SS BOND : bond 0.00268 / 0.16 ( 5) SS BOND : angle 0.53845 / 0.27 ( 10) hydrogen bonds : bond 0.04410 / 2.90 ( 1895) hydrogen bonds : angle 4.26448 / 3.11 ( 5328) metal coordination : bond 0.01613 / 0.81 ( 4) metal coordination : angle 4.85999 / 2.75 ( 3) Misc. bond : bond 0.23694 / 14.04 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 301 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: P 147 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.6792 (ttm170) REVERT: P 202 ARG cc_start: 0.8379 (ttp-110) cc_final: 0.8166 (ttp-110) REVERT: G 9 LYS cc_start: 0.8886 (mttp) cc_final: 0.8568 (ttpt) REVERT: G 115 GLU cc_start: 0.8955 (tt0) cc_final: 0.8523 (tt0) REVERT: F 84 GLU cc_start: 0.8634 (tt0) cc_final: 0.8116 (mt-10) REVERT: F 88 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8125 (mm-30) REVERT: F 100 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7976 (mm-30) REVERT: F 116 HIS cc_start: 0.8233 (m-70) cc_final: 0.7186 (m-70) REVERT: F 122 ASP cc_start: 0.8593 (p0) cc_final: 0.8343 (p0) REVERT: A 97 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: A 397 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8103 (mt) REVERT: B 353 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: B 364 MET cc_start: 0.8870 (tpp) cc_final: 0.8526 (tpp) REVERT: I 30 ASP cc_start: 0.9055 (t70) cc_final: 0.8820 (t70) REVERT: J 58 GLN cc_start: 0.8569 (mt0) cc_final: 0.8236 (mt0) REVERT: J 73 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8526 (ptt180) REVERT: M 364 MET cc_start: 0.8612 (tpp) cc_final: 0.8203 (tpt) REVERT: U 10 LYS cc_start: 0.9040 (tptp) cc_final: 0.8768 (tptt) REVERT: U 55 ARG cc_start: 0.9084 (ttm110) cc_final: 0.8790 (ttp-170) REVERT: U 73 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8309 (ptp-170) outliers start: 41 outliers final: 19 residues processed: 329 average time/residue: 0.8230 time to fit residues: 315.0791 Evaluate side-chains 312 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 287 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 147 ARG Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 292 GLU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 357 SER Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 297 optimal weight: 0.7980 chunk 266 optimal weight: 0.7980 chunk 352 optimal weight: 20.0000 chunk 153 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 244 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 289 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 193 HIS F 116 HIS B 377 ASN M 121 GLN O 90 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.075406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.057134 restraints weight = 56423.169| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 1.64 r_work: 0.2612 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9363 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.358 33383 Z= 0.107 Angle : 0.508 12.620 45365 Z= 0.247 Chirality : 0.040 0.140 4962 Planarity : 0.004 0.050 5700 Dihedral : 9.830 89.513 4822 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.02 % Allowed : 12.06 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.14), residues: 3955 helix: 2.12 (0.11), residues: 2184 sheet: 1.04 (0.27), residues: 359 loop : 0.77 (0.18), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 61 TYR 0.014 0.001 TYR N 225 PHE 0.018 0.001 PHE L 334 TRP 0.014 0.001 TRP C 142 HIS 0.012 0.001 HIS F 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (33367) covalent geometry : angle 0.50673 / 0.25 (45352) SS BOND : bond 0.00204 / 0.12 ( 5) SS BOND : angle 0.47368 / 0.24 ( 10) hydrogen bonds : bond 0.04012 / 2.64 ( 1895) hydrogen bonds : angle 4.17119 / 3.04 ( 5328) metal coordination : bond 0.00981 / 0.49 ( 4) metal coordination : angle 4.46013 / 2.50 ( 3) Misc. bond : bond 0.22862 / 13.75 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 309 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 112 LEU cc_start: 0.9088 (tp) cc_final: 0.8880 (tp) REVERT: G 9 LYS cc_start: 0.8867 (mttp) cc_final: 0.8547 (ttpt) REVERT: F 84 GLU cc_start: 0.8654 (tt0) cc_final: 0.8128 (mt-10) REVERT: F 88 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8134 (mm-30) REVERT: F 103 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8231 (pp20) REVERT: F 122 ASP cc_start: 0.8591 (p0) cc_final: 0.8340 (p0) REVERT: A 97 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: A 397 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8030 (mt) REVERT: B 364 MET cc_start: 0.8831 (tpp) cc_final: 0.8461 (tpp) REVERT: J 58 GLN cc_start: 0.8592 (mt0) cc_final: 0.8270 (mt0) REVERT: J 74 GLU cc_start: 0.7891 (pm20) cc_final: 0.7668 (pp20) REVERT: M 34 ILE cc_start: 0.8826 (pt) cc_final: 0.8611 (mm) REVERT: M 364 MET cc_start: 0.8566 (tpp) cc_final: 0.8124 (tpt) REVERT: U 10 LYS cc_start: 0.9030 (tptp) cc_final: 0.8774 (tptt) REVERT: U 55 ARG cc_start: 0.9077 (ttm110) cc_final: 0.8764 (ttp-170) outliers start: 34 outliers final: 14 residues processed: 332 average time/residue: 0.8435 time to fit residues: 324.5602 Evaluate side-chains 312 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 295 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 357 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 132 optimal weight: 0.6980 chunk 183 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 304 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 377 ASN O 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.073912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.055430 restraints weight = 56796.772| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 1.65 r_work: 0.2573 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9392 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.351 33383 Z= 0.149 Angle : 0.546 14.629 45365 Z= 0.264 Chirality : 0.041 0.143 4962 Planarity : 0.004 0.051 5700 Dihedral : 9.851 89.439 4822 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.90 % Allowed : 12.63 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.14), residues: 3955 helix: 2.12 (0.11), residues: 2174 sheet: 1.05 (0.27), residues: 359 loop : 0.74 (0.18), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 236 TYR 0.018 0.001 TYR N 225 PHE 0.020 0.001 PHE A 334 TRP 0.015 0.001 TRP C 142 HIS 0.010 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (33367) covalent geometry : angle 0.54485 / 0.26 (45352) SS BOND : bond 0.00214 / 0.13 ( 5) SS BOND : angle 0.46071 / 0.23 ( 10) hydrogen bonds : bond 0.04506 / 2.97 ( 1895) hydrogen bonds : angle 4.22181 / 3.08 ( 5328) metal coordination : bond 0.01739 / 0.87 ( 4) metal coordination : angle 4.72655 / 2.69 ( 3) Misc. bond : bond 0.23860 / 14.02 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 297 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 112 LEU cc_start: 0.9125 (tp) cc_final: 0.8921 (tp) REVERT: G 9 LYS cc_start: 0.8897 (mttp) cc_final: 0.8568 (ttpt) REVERT: G 115 GLU cc_start: 0.8948 (tt0) cc_final: 0.8499 (tt0) REVERT: F 84 GLU cc_start: 0.8657 (tt0) cc_final: 0.8089 (mt-10) REVERT: F 88 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8160 (mm-30) REVERT: F 103 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8246 (pp20) REVERT: F 122 ASP cc_start: 0.8627 (p0) cc_final: 0.8375 (p0) REVERT: A 97 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: A 397 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8022 (mt) REVERT: B 353 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: B 364 MET cc_start: 0.8855 (tpp) cc_final: 0.8474 (tpp) REVERT: J 58 GLN cc_start: 0.8562 (mt0) cc_final: 0.8260 (mt0) REVERT: M 364 MET cc_start: 0.8579 (tpp) cc_final: 0.8145 (tpt) REVERT: U 55 ARG cc_start: 0.9086 (ttm110) cc_final: 0.8787 (ttp-170) outliers start: 30 outliers final: 19 residues processed: 319 average time/residue: 0.8322 time to fit residues: 307.5858 Evaluate side-chains 314 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 291 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 357 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 344 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 389 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 307 optimal weight: 5.9990 chunk 341 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 294 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 115 ASN B 316 GLN B 377 ASN N 11 ASN O 90 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.072164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.053611 restraints weight = 56743.522| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 1.65 r_work: 0.2532 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2421 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9417 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.370 33383 Z= 0.225 Angle : 0.601 14.630 45365 Z= 0.293 Chirality : 0.044 0.154 4962 Planarity : 0.004 0.050 5700 Dihedral : 10.123 89.854 4822 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.05 % Allowed : 12.60 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.14), residues: 3955 helix: 2.01 (0.11), residues: 2156 sheet: 0.96 (0.27), residues: 361 loop : 0.68 (0.18), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 236 TYR 0.023 0.002 TYR C 225 PHE 0.023 0.002 PHE C 240 TRP 0.019 0.001 TRP C 142 HIS 0.011 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.22 (33367) covalent geometry : angle 0.59983 / 0.29 (45352) SS BOND : bond 0.00283 / 0.17 ( 5) SS BOND : angle 0.57991 / 0.29 ( 10) hydrogen bonds : bond 0.05184 / 3.42 ( 1895) hydrogen bonds : angle 4.36490 / 3.18 ( 5328) metal coordination : bond 0.02685 / 1.34 ( 4) metal coordination : angle 5.23637 / 2.94 ( 3) Misc. bond : bond 0.26007 / 15.10 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 283 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: G 9 LYS cc_start: 0.8889 (mttp) cc_final: 0.8589 (ttpt) REVERT: F 84 GLU cc_start: 0.8640 (tt0) cc_final: 0.8162 (mt-10) REVERT: F 103 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8290 (pp20) REVERT: F 122 ASP cc_start: 0.8697 (p0) cc_final: 0.8465 (p0) REVERT: A 97 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: A 426 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8770 (mttm) REVERT: B 353 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: B 364 MET cc_start: 0.8877 (tpp) cc_final: 0.8573 (tpp) REVERT: J 58 GLN cc_start: 0.8580 (mt0) cc_final: 0.8259 (mt0) REVERT: U 55 ARG cc_start: 0.9119 (ttm110) cc_final: 0.8826 (ttp-170) outliers start: 35 outliers final: 22 residues processed: 307 average time/residue: 0.8191 time to fit residues: 291.3701 Evaluate side-chains 306 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 280 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 201 ARG Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 357 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 266 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 255 optimal weight: 6.9990 chunk 362 optimal weight: 0.0010 chunk 22 optimal weight: 0.9980 chunk 294 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 250 optimal weight: 2.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 115 ASN F 97 HIS B 377 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.073675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.055288 restraints weight = 56154.815| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 1.64 r_work: 0.2572 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9394 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.377 33383 Z= 0.135 Angle : 0.546 14.116 45365 Z= 0.264 Chirality : 0.041 0.148 4962 Planarity : 0.004 0.051 5700 Dihedral : 9.841 89.033 4822 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.87 % Allowed : 12.69 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.14), residues: 3955 helix: 2.05 (0.11), residues: 2174 sheet: 0.99 (0.27), residues: 361 loop : 0.75 (0.18), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 236 TYR 0.017 0.001 TYR N 225 PHE 0.020 0.001 PHE L 334 TRP 0.015 0.001 TRP C 142 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (33367) covalent geometry : angle 0.54422 / 0.26 (45352) SS BOND : bond 0.00247 / 0.14 ( 5) SS BOND : angle 0.49405 / 0.24 ( 10) hydrogen bonds : bond 0.04487 / 2.95 ( 1895) hydrogen bonds : angle 4.27367 / 3.12 ( 5328) metal coordination : bond 0.01419 / 0.71 ( 4) metal coordination : angle 4.77212 / 2.66 ( 3) Misc. bond : bond 0.24973 / 14.59 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 294 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: G 9 LYS cc_start: 0.8873 (mttp) cc_final: 0.8567 (ttpt) REVERT: F 84 GLU cc_start: 0.8650 (tt0) cc_final: 0.8120 (mt-10) REVERT: F 88 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8143 (mm-30) REVERT: F 122 ASP cc_start: 0.8702 (p0) cc_final: 0.8440 (p0) REVERT: A 97 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: A 397 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7975 (mt) REVERT: A 426 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8776 (mttm) REVERT: B 353 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: B 364 MET cc_start: 0.8869 (tpp) cc_final: 0.8536 (tpp) REVERT: J 58 GLN cc_start: 0.8577 (mt0) cc_final: 0.8265 (mt0) REVERT: O 248 MET cc_start: 0.9103 (ttp) cc_final: 0.8766 (ttm) REVERT: U 55 ARG cc_start: 0.9094 (ttm110) cc_final: 0.8892 (tpp-160) outliers start: 29 outliers final: 19 residues processed: 315 average time/residue: 0.7699 time to fit residues: 281.7130 Evaluate side-chains 312 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 289 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 292 GLU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 357 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 13 optimal weight: 6.9990 chunk 252 optimal weight: 1.9990 chunk 162 optimal weight: 0.0000 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 115 ASN B 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.073373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.054930 restraints weight = 56630.572| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 1.65 r_work: 0.2564 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9397 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.368 33383 Z= 0.154 Angle : 0.562 14.251 45365 Z= 0.270 Chirality : 0.042 0.147 4962 Planarity : 0.004 0.051 5700 Dihedral : 9.787 88.559 4822 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.75 % Allowed : 12.78 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.14), residues: 3955 helix: 2.08 (0.11), residues: 2162 sheet: 1.04 (0.27), residues: 359 loop : 0.75 (0.18), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 236 TYR 0.019 0.001 TYR N 225 PHE 0.021 0.001 PHE A 334 TRP 0.016 0.001 TRP C 142 HIS 0.010 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (33367) covalent geometry : angle 0.56054 / 0.27 (45352) SS BOND : bond 0.00266 / 0.15 ( 5) SS BOND : angle 0.53495 / 0.26 ( 10) hydrogen bonds : bond 0.04622 / 3.05 ( 1895) hydrogen bonds : angle 4.27162 / 3.12 ( 5328) metal coordination : bond 0.01719 / 0.86 ( 4) metal coordination : angle 4.67718 / 2.63 ( 3) Misc. bond : bond 0.25783 / 14.77 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 289 time to evaluate : 1.291 Fit side-chains revert: symmetry clash REVERT: P 112 LEU cc_start: 0.9114 (tp) cc_final: 0.8876 (tp) REVERT: P 147 ARG cc_start: 0.7725 (ttm170) cc_final: 0.7406 (ttm170) REVERT: G 9 LYS cc_start: 0.8907 (mttp) cc_final: 0.8578 (ttpt) REVERT: F 84 GLU cc_start: 0.8618 (tt0) cc_final: 0.8089 (mt-10) REVERT: F 88 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8110 (mm-30) REVERT: F 122 ASP cc_start: 0.8703 (p0) cc_final: 0.8453 (p0) REVERT: A 97 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: A 426 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8766 (mttm) REVERT: B 353 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: B 364 MET cc_start: 0.8866 (tpp) cc_final: 0.8528 (tpp) REVERT: D 85 MET cc_start: 0.8635 (mtm) cc_final: 0.8117 (ptp) REVERT: J 58 GLN cc_start: 0.8572 (mt0) cc_final: 0.8265 (mt0) REVERT: O 248 MET cc_start: 0.9260 (ttp) cc_final: 0.8758 (ttm) REVERT: U 55 ARG cc_start: 0.9103 (ttm110) cc_final: 0.8796 (ttp-170) outliers start: 25 outliers final: 21 residues processed: 308 average time/residue: 0.7625 time to fit residues: 271.7505 Evaluate side-chains 313 residues out of total 3325 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 289 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 292 GLU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 357 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 179 optimal weight: 3.9990 chunk 354 optimal weight: 2.9990 chunk 387 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 370 optimal weight: 3.9990 chunk 229 optimal weight: 0.6980 chunk 209 optimal weight: 7.9990 chunk 377 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 234 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.074780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.056427 restraints weight = 56718.767| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 1.66 r_work: 0.2595 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9376 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.362 33383 Z= 0.114 Angle : 0.530 13.195 45365 Z= 0.256 Chirality : 0.040 0.144 4962 Planarity : 0.004 0.051 5700 Dihedral : 9.548 89.654 4822 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.66 % Allowed : 13.02 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.14), residues: 3955 helix: 2.11 (0.11), residues: 2174 sheet: 1.06 (0.27), residues: 359 loop : 0.80 (0.18), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 236 TYR 0.014 0.001 TYR C 225 PHE 0.019 0.001 PHE A 334 TRP 0.015 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (33367) covalent geometry : angle 0.52847 / 0.26 (45352) SS BOND : bond 0.00250 / 0.14 ( 5) SS BOND : angle 0.49100 / 0.24 ( 10) hydrogen bonds : bond 0.04169 / 2.74 ( 1895) hydrogen bonds : angle 4.20347 / 3.07 ( 5328) metal coordination : bond 0.00873 / 0.44 ( 4) metal coordination : angle 4.26952 / 2.39 ( 3) Misc. bond : bond 0.22984 / 13.69 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13274.02 seconds wall clock time: 226 minutes 39.22 seconds (13599.22 seconds total)