Starting phenix.real_space_refine on Tue Jul 23 01:32:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umt_42383/07_2024/8umt_42383_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umt_42383/07_2024/8umt_42383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umt_42383/07_2024/8umt_42383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umt_42383/07_2024/8umt_42383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umt_42383/07_2024/8umt_42383_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umt_42383/07_2024/8umt_42383_neut.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.045 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 P 11 5.49 5 Mg 3 5.21 5 S 135 5.16 5 C 13022 2.51 5 N 3568 2.21 5 O 3958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 171": "NH1" <-> "NH2" Residue "D GLU 259": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "F TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 85": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20697 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4255 Classifications: {'peptide': 537} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 504} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2492 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain: "C" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2563 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain: "D" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2512 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "E" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2745 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 15, 'TRANS': 329} Chain: "F" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1989 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "H" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.64, per 1000 atoms: 0.56 Number of scatterers: 20697 At special positions: 0 Unit cell: (115.92, 120.888, 147.384, 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) S 135 16.00 P 11 15.00 Mg 3 11.99 O 3958 8.00 N 3568 7.00 C 13022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.90 Conformation dependent library (CDL) restraints added in 3.9 seconds 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4994 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 15 sheets defined 50.4% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 311 through 314 Processing helix chain 'A' and resid 347 through 355 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 405 through 414 Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'A' and resid 501 through 505 removed outlier: 3.542A pdb=" N ALA A 505 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 530 removed outlier: 3.780A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 549 through 563 Processing helix chain 'A' and resid 568 through 573 removed outlier: 3.584A pdb=" N VAL A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 595 removed outlier: 3.571A pdb=" N GLN A 591 " --> pdb=" O PHE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 642 Processing helix chain 'A' and resid 645 through 656 Processing helix chain 'A' and resid 668 through 690 Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.734A pdb=" N VAL A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 704 " --> pdb=" O PHE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 744 Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.697A pdb=" N SER A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 Processing helix chain 'A' and resid 761 through 769 Processing helix chain 'A' and resid 782 through 800 Processing helix chain 'A' and resid 820 through 825 removed outlier: 3.971A pdb=" N LEU A 824 " --> pdb=" O ASN A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 863 Processing helix chain 'B' and resid 37 through 42 removed outlier: 3.628A pdb=" N TYR B 42 " --> pdb=" O TRP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 54 through 67 removed outlier: 3.687A pdb=" N ARG B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.889A pdb=" N VAL B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 removed outlier: 4.204A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.743A pdb=" N ARG B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 210 Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 256 removed outlier: 4.029A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.968A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 Processing helix chain 'B' and resid 333 through 348 removed outlier: 3.759A pdb=" N MET B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 37 through 50 removed outlier: 3.580A pdb=" N GLU C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 removed outlier: 3.624A pdb=" N ILE C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 127 through 130 removed outlier: 3.607A pdb=" N MET C 130 " --> pdb=" O ALA C 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 127 through 130' Processing helix chain 'C' and resid 131 through 145 Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.666A pdb=" N LYS C 160 " --> pdb=" O TYR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 178 through 193 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 198 through 209 Processing helix chain 'C' and resid 212 through 227 removed outlier: 3.527A pdb=" N ALA C 216 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 256 Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 276 through 288 Processing helix chain 'C' and resid 294 through 314 Processing helix chain 'C' and resid 317 through 340 removed outlier: 4.024A pdb=" N GLN C 321 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 55 through 69 removed outlier: 3.701A pdb=" N ALA D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 104 Proline residue: D 98 - end of helix removed outlier: 4.345A pdb=" N ARG D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 128 removed outlier: 3.947A pdb=" N VAL D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 155 removed outlier: 3.627A pdb=" N MET D 155 " --> pdb=" O ALA D 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 152 through 155' Processing helix chain 'D' and resid 156 through 170 Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.603A pdb=" N ARG D 185 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 193 removed outlier: 3.663A pdb=" N ARG D 193 " --> pdb=" O PRO D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'D' and resid 223 through 234 Processing helix chain 'D' and resid 237 through 253 Processing helix chain 'D' and resid 258 through 266 removed outlier: 3.788A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 283 removed outlier: 3.577A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'D' and resid 320 through 341 Processing helix chain 'D' and resid 343 through 360 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.624A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.850A pdb=" N GLU E 65 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 100 removed outlier: 3.847A pdb=" N ASP E 99 " --> pdb=" O ASN E 96 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA E 100 " --> pdb=" O PRO E 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 96 through 100' Processing helix chain 'E' and resid 103 through 117 removed outlier: 3.837A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 155 Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 222 through 237 removed outlier: 3.654A pdb=" N CYS E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.948A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 Processing helix chain 'E' and resid 287 through 301 Processing helix chain 'E' and resid 306 through 323 removed outlier: 4.165A pdb=" N GLU E 310 " --> pdb=" O GLN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 349 removed outlier: 4.248A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.859A pdb=" N ILE F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY F 155 " --> pdb=" O LEU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 218 through 222 removed outlier: 3.838A pdb=" N SER F 222 " --> pdb=" O THR F 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 20 removed outlier: 4.510A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 222 Proline residue: G 220 - end of helix No H-bonds generated for 'chain 'G' and resid 217 through 222' Processing helix chain 'H' and resid 8 through 10 No H-bonds generated for 'chain 'H' and resid 8 through 10' Processing helix chain 'H' and resid 11 through 16 Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 72 through 79 removed outlier: 3.568A pdb=" N LYS H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 190 through 194 removed outlier: 4.012A pdb=" N GLU H 193 " --> pdb=" O LYS H 190 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA H 194 " --> pdb=" O GLU H 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 190 through 194' Processing helix chain 'H' and resid 209 through 217 Processing helix chain 'H' and resid 218 through 222 removed outlier: 3.857A pdb=" N LEU H 221 " --> pdb=" O ALA H 218 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER H 222 " --> pdb=" O THR H 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 218 through 222' Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 180 Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 399 removed outlier: 5.888A pdb=" N SER A 394 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A 433 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 396 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ASP A 435 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET A 398 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N ILE A 487 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU A 432 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE A 489 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE A 434 " --> pdb=" O ILE A 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 532 through 533 removed outlier: 7.933A pdb=" N ARG A 532 " --> pdb=" O LEU A 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 803 through 807 Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.227A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE B 73 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.566A pdb=" N LEU C 88 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASP C 125 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 90 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 122 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU C 57 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 196 through 197 removed outlier: 6.183A pdb=" N ASP C 196 " --> pdb=" O VAL C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 75 through 77 removed outlier: 5.673A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU D 106 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASP D 150 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU D 108 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 68 through 75 removed outlier: 6.192A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 59 through 62 removed outlier: 4.212A pdb=" N THR F 59 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN G 177 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 71 removed outlier: 7.260A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N SER F 230 " --> pdb=" O PRO F 234 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 204 through 208 removed outlier: 5.483A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL F 167 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR H 59 " --> pdb=" O ARG H 5 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 60 through 61 removed outlier: 3.860A pdb=" N VAL G 111 " --> pdb=" O LYS H 181 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS H 181 " --> pdb=" O VAL G 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 66 through 71 removed outlier: 5.969A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 71 removed outlier: 3.592A pdb=" N LEU H 66 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) 1103 hydrogen bonds defined for protein. 3177 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: 7.28 Time building geometry restraints manager: 8.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 6966 1.36 - 1.51: 5077 1.51 - 1.65: 8779 1.65 - 1.80: 120 1.80 - 1.95: 85 Bond restraints: 21027 Sorted by residual: bond pdb=" CA LYS H 217 " pdb=" C LYS H 217 " ideal model delta sigma weight residual 1.522 1.583 -0.061 1.43e-02 4.89e+03 1.83e+01 bond pdb=" N PHE D 54 " pdb=" CA PHE D 54 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" N LEU G 12 " pdb=" CA LEU G 12 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.23e-02 6.61e+03 8.05e+00 bond pdb=" N VAL A 180 " pdb=" CA VAL A 180 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.89e+00 bond pdb=" N GLU H 85 " pdb=" CA GLU H 85 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.14e-02 7.69e+03 7.58e+00 ... (remaining 21022 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.49: 592 106.49 - 113.89: 12097 113.89 - 121.30: 10350 121.30 - 128.70: 5306 128.70 - 136.10: 109 Bond angle restraints: 28454 Sorted by residual: angle pdb=" N TYR E 343 " pdb=" CA TYR E 343 " pdb=" C TYR E 343 " ideal model delta sigma weight residual 111.14 106.05 5.09 1.08e+00 8.57e-01 2.22e+01 angle pdb=" N ASP F 156 " pdb=" CA ASP F 156 " pdb=" C ASP F 156 " ideal model delta sigma weight residual 114.31 108.23 6.08 1.29e+00 6.01e-01 2.22e+01 angle pdb=" C THR A 417 " pdb=" N GLN A 418 " pdb=" CA GLN A 418 " ideal model delta sigma weight residual 122.61 129.22 -6.61 1.56e+00 4.11e-01 1.80e+01 angle pdb=" C GLY E 33 " pdb=" N ASP E 34 " pdb=" CA ASP E 34 " ideal model delta sigma weight residual 122.82 128.83 -6.01 1.42e+00 4.96e-01 1.79e+01 angle pdb=" N GLU D 188 " pdb=" CA GLU D 188 " pdb=" C GLU D 188 " ideal model delta sigma weight residual 113.25 118.71 -5.46 1.30e+00 5.92e-01 1.76e+01 ... (remaining 28449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.19: 12342 26.19 - 52.37: 576 52.37 - 78.56: 71 78.56 - 104.75: 6 104.75 - 130.93: 2 Dihedral angle restraints: 12997 sinusoidal: 5323 harmonic: 7674 Sorted by residual: dihedral pdb=" C5' ADP E2000 " pdb=" O5' ADP E2000 " pdb=" PA ADP E2000 " pdb=" O2A ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 169.07 130.93 1 2.00e+01 2.50e-03 3.97e+01 dihedral pdb=" O1B ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PB ADP E2000 " pdb=" PA ADP E2000 " ideal model delta sinusoidal sigma weight residual -60.00 -163.80 103.80 1 2.00e+01 2.50e-03 2.97e+01 dihedral pdb=" CA VAL F 236 " pdb=" C VAL F 236 " pdb=" N VAL F 237 " pdb=" CA VAL F 237 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 12994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2532 0.051 - 0.103: 608 0.103 - 0.154: 156 0.154 - 0.206: 19 0.206 - 0.257: 2 Chirality restraints: 3317 Sorted by residual: chirality pdb=" CA GLU D 188 " pdb=" N GLU D 188 " pdb=" C GLU D 188 " pdb=" CB GLU D 188 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA LEU H 50 " pdb=" N LEU H 50 " pdb=" C LEU H 50 " pdb=" CB LEU H 50 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB ILE H 241 " pdb=" CA ILE H 241 " pdb=" CG1 ILE H 241 " pdb=" CG2 ILE H 241 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.06e-01 ... (remaining 3314 not shown) Planarity restraints: 3643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 698 " -0.065 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO A 699 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 699 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 699 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 293 " -0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C GLU A 293 " 0.065 2.00e-02 2.50e+03 pdb=" O GLU A 293 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU A 294 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 76 " 0.051 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO E 77 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO E 77 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 77 " 0.043 5.00e-02 4.00e+02 ... (remaining 3640 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 214 2.62 - 3.19: 16863 3.19 - 3.76: 32679 3.76 - 4.33: 43253 4.33 - 4.90: 71982 Nonbonded interactions: 164991 Sorted by model distance: nonbonded pdb="MG MG B 401 " pdb=" O1B AGS B 402 " model vdw 2.048 2.170 nonbonded pdb="MG MG B 401 " pdb=" O2G AGS B 402 " model vdw 2.071 2.170 nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.080 2.170 nonbonded pdb="MG MG D 401 " pdb=" O3G AGS D 402 " model vdw 2.082 2.170 nonbonded pdb="MG MG B 401 " pdb=" O1A AGS B 402 " model vdw 2.107 2.170 ... (remaining 164986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 258) selection = (chain 'H' and resid 1 through 258) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 54.960 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 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 : 0.004 0.064 21027 Z= 0.244 Angle : 0.750 9.857 28454 Z= 0.424 Chirality : 0.048 0.257 3317 Planarity : 0.007 0.098 3643 Dihedral : 14.616 130.935 8003 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 4.14 % Allowed : 11.52 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.15), residues: 2601 helix: -1.46 (0.12), residues: 1208 sheet: -0.65 (0.23), residues: 513 loop : -1.46 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 28 HIS 0.005 0.001 HIS C 55 PHE 0.015 0.002 PHE F 169 TYR 0.012 0.001 TYR D 77 ARG 0.003 0.000 ARG C 311 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 473 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 MET cc_start: 0.5988 (tpp) cc_final: 0.5637 (tpp) REVERT: A 843 LEU cc_start: 0.8676 (tp) cc_final: 0.8456 (tp) REVERT: B 38 TRP cc_start: 0.7185 (m-10) cc_final: 0.6970 (m-10) REVERT: B 245 PHE cc_start: 0.7011 (t80) cc_final: 0.6803 (t80) REVERT: D 238 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8210 (tt) REVERT: E 155 TYR cc_start: 0.5786 (m-80) cc_final: 0.5368 (m-80) REVERT: F 1 MET cc_start: 0.4277 (ppp) cc_final: 0.3349 (ppp) REVERT: F 14 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8114 (ttpp) REVERT: G 87 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6517 (pp) REVERT: G 154 ILE cc_start: 0.5604 (OUTLIER) cc_final: 0.5279 (tp) outliers start: 95 outliers final: 21 residues processed: 545 average time/residue: 0.3577 time to fit residues: 288.5778 Evaluate side-chains 341 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 317 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 GLN E 194 HIS E 213 HIS F 177 ASN G 36 ASN G 65 ASN G 213 ASN G 246 HIS H 131 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 21027 Z= 0.463 Angle : 0.786 10.679 28454 Z= 0.400 Chirality : 0.048 0.181 3317 Planarity : 0.006 0.080 3643 Dihedral : 8.537 134.242 2936 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.24 % Allowed : 15.92 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.16), residues: 2601 helix: -0.56 (0.14), residues: 1228 sheet: -0.70 (0.23), residues: 536 loop : -1.19 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP H 28 HIS 0.018 0.002 HIS F 153 PHE 0.030 0.003 PHE H 207 TYR 0.022 0.003 TYR B 279 ARG 0.013 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 349 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6749 (pm20) REVERT: D 193 ARG cc_start: 0.7405 (mmm160) cc_final: 0.7180 (mmm-85) REVERT: F 1 MET cc_start: 0.4813 (ppp) cc_final: 0.3942 (ppp) REVERT: F 14 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8409 (mtpp) REVERT: F 60 TYR cc_start: 0.3066 (t80) cc_final: 0.2833 (t80) REVERT: G 87 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7194 (pp) REVERT: G 154 ILE cc_start: 0.5965 (OUTLIER) cc_final: 0.5552 (tp) REVERT: H 184 GLN cc_start: 0.6168 (tm-30) cc_final: 0.5941 (tm-30) outliers start: 120 outliers final: 84 residues processed: 434 average time/residue: 0.3545 time to fit residues: 230.0333 Evaluate side-chains 392 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 305 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 235 optimal weight: 4.9990 chunk 254 optimal weight: 0.9990 chunk 209 optimal weight: 0.9980 chunk 233 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 chunk 189 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN B 126 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 HIS G 213 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21027 Z= 0.184 Angle : 0.610 9.116 28454 Z= 0.307 Chirality : 0.042 0.242 3317 Planarity : 0.005 0.079 3643 Dihedral : 7.890 121.288 2920 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.75 % Allowed : 18.67 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2601 helix: 0.19 (0.15), residues: 1232 sheet: -0.56 (0.23), residues: 514 loop : -1.02 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 307 HIS 0.013 0.001 HIS F 153 PHE 0.018 0.002 PHE A 506 TYR 0.017 0.001 TYR E 254 ARG 0.010 0.000 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 343 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.4793 (ppp) cc_final: 0.4018 (ppp) REVERT: F 14 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8249 (mtpp) REVERT: F 144 PHE cc_start: 0.7875 (t80) cc_final: 0.7388 (t80) REVERT: F 148 CYS cc_start: 0.7733 (m) cc_final: 0.7405 (m) REVERT: F 199 MET cc_start: 0.4386 (mpp) cc_final: 0.4073 (pmm) REVERT: G 13 LYS cc_start: 0.8166 (ttmm) cc_final: 0.7737 (mttp) REVERT: G 87 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.7037 (pp) REVERT: G 151 LEU cc_start: 0.7964 (tp) cc_final: 0.7706 (tp) REVERT: G 154 ILE cc_start: 0.5929 (OUTLIER) cc_final: 0.5562 (tp) outliers start: 86 outliers final: 59 residues processed: 397 average time/residue: 0.3600 time to fit residues: 213.2171 Evaluate side-chains 360 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 299 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 560 TYR Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 155 TYR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 158 optimal weight: 7.9990 chunk 236 optimal weight: 8.9990 chunk 250 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 224 optimal weight: 30.0000 chunk 67 optimal weight: 4.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS E 213 HIS ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN ** H 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 21027 Z= 0.451 Angle : 0.769 10.790 28454 Z= 0.391 Chirality : 0.048 0.201 3317 Planarity : 0.006 0.075 3643 Dihedral : 8.152 132.227 2917 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.85 % Allowed : 18.89 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2601 helix: -0.19 (0.14), residues: 1226 sheet: -0.77 (0.22), residues: 535 loop : -1.11 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 307 HIS 0.010 0.001 HIS C 289 PHE 0.028 0.003 PHE E 339 TYR 0.020 0.002 TYR E 318 ARG 0.009 0.001 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 318 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6640 (pm20) REVERT: A 409 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: A 839 GLN cc_start: 0.6943 (pm20) cc_final: 0.6713 (pm20) REVERT: A 853 MET cc_start: 0.8710 (mmm) cc_final: 0.8430 (mmp) REVERT: E 119 GLN cc_start: 0.6450 (OUTLIER) cc_final: 0.5428 (pm20) REVERT: F 1 MET cc_start: 0.5048 (ppp) cc_final: 0.4206 (ppp) REVERT: F 144 PHE cc_start: 0.8051 (t80) cc_final: 0.7748 (t80) REVERT: G 87 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7265 (pp) outliers start: 134 outliers final: 96 residues processed: 421 average time/residue: 0.3353 time to fit residues: 216.9039 Evaluate side-chains 387 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 287 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 799 TYR Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 357 GLN Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 186 optimal weight: 40.0000 chunk 103 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 224 optimal weight: 30.0000 chunk 63 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS E 213 HIS ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21027 Z= 0.214 Angle : 0.635 9.796 28454 Z= 0.319 Chirality : 0.043 0.275 3317 Planarity : 0.005 0.077 3643 Dihedral : 7.800 118.971 2914 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.54 % Allowed : 20.90 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2601 helix: 0.40 (0.15), residues: 1227 sheet: -0.56 (0.23), residues: 522 loop : -1.01 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 307 HIS 0.008 0.001 HIS F 153 PHE 0.028 0.002 PHE E 339 TYR 0.016 0.001 TYR G 211 ARG 0.007 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 319 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: A 531 MET cc_start: 0.6919 (tpp) cc_final: 0.6644 (tpp) REVERT: A 853 MET cc_start: 0.8704 (mmm) cc_final: 0.8457 (mmp) REVERT: D 240 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8316 (mtpp) REVERT: D 246 GLN cc_start: 0.6440 (tp40) cc_final: 0.6137 (tp40) REVERT: E 119 GLN cc_start: 0.6413 (OUTLIER) cc_final: 0.5404 (pm20) REVERT: F 1 MET cc_start: 0.4879 (ppp) cc_final: 0.4128 (ppp) REVERT: F 144 PHE cc_start: 0.7942 (t80) cc_final: 0.7617 (t80) REVERT: F 199 MET cc_start: 0.3806 (pmm) cc_final: 0.3488 (pmm) REVERT: G 13 LYS cc_start: 0.8218 (ttmm) cc_final: 0.7755 (mttp) REVERT: G 87 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.6942 (pp) REVERT: G 154 ILE cc_start: 0.6065 (OUTLIER) cc_final: 0.5640 (tp) REVERT: G 210 ARG cc_start: 0.6723 (ptm-80) cc_final: 0.6479 (ppt170) REVERT: H 244 MET cc_start: 0.6533 (ptp) cc_final: 0.6303 (ptm) outliers start: 104 outliers final: 84 residues processed: 389 average time/residue: 0.3701 time to fit residues: 217.8996 Evaluate side-chains 382 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 293 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 155 TYR Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 8.9990 chunk 225 optimal weight: 4.9990 chunk 49 optimal weight: 0.1980 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 250 optimal weight: 8.9990 chunk 208 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 194 HIS E 213 HIS G 36 ASN G 49 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN ** H 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 21027 Z= 0.283 Angle : 0.650 12.106 28454 Z= 0.328 Chirality : 0.044 0.295 3317 Planarity : 0.005 0.073 3643 Dihedral : 7.749 118.421 2913 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 5.72 % Allowed : 20.29 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2601 helix: 0.40 (0.15), residues: 1229 sheet: -0.55 (0.23), residues: 519 loop : -0.98 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 307 HIS 0.006 0.001 HIS F 153 PHE 0.038 0.002 PHE F 215 TYR 0.017 0.002 TYR B 213 ARG 0.007 0.001 ARG G 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 313 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: A 531 MET cc_start: 0.6976 (tpp) cc_final: 0.6590 (tpp) REVERT: A 853 MET cc_start: 0.8700 (mmm) cc_final: 0.8461 (mmp) REVERT: B 102 MET cc_start: 0.7882 (tpp) cc_final: 0.7076 (tpt) REVERT: C 106 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.6075 (tp) REVERT: C 309 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6777 (tt0) REVERT: D 240 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8351 (mtpp) REVERT: D 246 GLN cc_start: 0.6483 (tp40) cc_final: 0.6169 (tp-100) REVERT: E 119 GLN cc_start: 0.6432 (OUTLIER) cc_final: 0.5440 (pm20) REVERT: F 1 MET cc_start: 0.4968 (ppp) cc_final: 0.4192 (ppp) REVERT: F 144 PHE cc_start: 0.8095 (t80) cc_final: 0.7598 (t80) REVERT: F 148 CYS cc_start: 0.7820 (m) cc_final: 0.7279 (m) REVERT: G 13 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7776 (mttp) REVERT: G 87 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7001 (pp) REVERT: G 154 ILE cc_start: 0.6324 (OUTLIER) cc_final: 0.5839 (tp) REVERT: H 30 ILE cc_start: 0.3998 (OUTLIER) cc_final: 0.3787 (mm) REVERT: H 244 MET cc_start: 0.6648 (ptp) cc_final: 0.6403 (ptm) outliers start: 131 outliers final: 104 residues processed: 404 average time/residue: 0.3473 time to fit residues: 212.0218 Evaluate side-chains 411 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 299 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 182 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 213 HIS G 125 GLN H 44 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21027 Z= 0.263 Angle : 0.649 12.087 28454 Z= 0.327 Chirality : 0.043 0.280 3317 Planarity : 0.005 0.075 3643 Dihedral : 7.561 119.181 2912 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.63 % Allowed : 20.94 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2601 helix: 0.49 (0.15), residues: 1230 sheet: -0.56 (0.23), residues: 512 loop : -0.95 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 307 HIS 0.006 0.001 HIS F 153 PHE 0.059 0.002 PHE F 215 TYR 0.018 0.002 TYR F 249 ARG 0.012 0.001 ARG E 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 317 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7915 (m-80) REVERT: A 531 MET cc_start: 0.6856 (tpp) cc_final: 0.6480 (tpp) REVERT: A 655 ASN cc_start: 0.7320 (OUTLIER) cc_final: 0.7069 (m110) REVERT: A 853 MET cc_start: 0.8699 (mmm) cc_final: 0.8482 (mmp) REVERT: B 102 MET cc_start: 0.7971 (tpp) cc_final: 0.7158 (tpt) REVERT: B 229 MET cc_start: 0.7272 (tpp) cc_final: 0.6884 (tpp) REVERT: C 106 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6110 (tp) REVERT: C 309 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6806 (tt0) REVERT: D 246 GLN cc_start: 0.6571 (tp40) cc_final: 0.6243 (tp-100) REVERT: E 119 GLN cc_start: 0.6409 (OUTLIER) cc_final: 0.5422 (pm20) REVERT: F 1 MET cc_start: 0.4981 (ppp) cc_final: 0.4209 (ppp) REVERT: F 90 LEU cc_start: 0.7471 (tp) cc_final: 0.7199 (tp) REVERT: F 144 PHE cc_start: 0.8132 (t80) cc_final: 0.7645 (t80) REVERT: F 148 CYS cc_start: 0.7828 (m) cc_final: 0.7322 (m) REVERT: G 13 LYS cc_start: 0.8205 (ttmm) cc_final: 0.7745 (mttp) REVERT: G 87 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.6968 (pp) REVERT: H 244 MET cc_start: 0.6675 (ptp) cc_final: 0.6449 (ptm) outliers start: 129 outliers final: 103 residues processed: 406 average time/residue: 0.3393 time to fit residues: 207.6169 Evaluate side-chains 399 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 290 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 54 PHE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 302 ASN Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 246 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 170 optimal weight: 0.5980 chunk 123 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 194 HIS E 213 HIS F 38 GLN F 65 ASN G 36 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21027 Z= 0.223 Angle : 0.640 12.873 28454 Z= 0.320 Chirality : 0.043 0.264 3317 Planarity : 0.005 0.074 3643 Dihedral : 7.381 119.583 2911 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 5.32 % Allowed : 21.42 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), residues: 2601 helix: 0.58 (0.15), residues: 1241 sheet: -0.54 (0.24), residues: 491 loop : -0.91 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 307 HIS 0.014 0.001 HIS G 153 PHE 0.033 0.002 PHE E 339 TYR 0.028 0.001 TYR F 114 ARG 0.008 0.000 ARG G 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 314 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: A 531 MET cc_start: 0.6843 (tpp) cc_final: 0.6439 (tpp) REVERT: A 655 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.7057 (m110) REVERT: A 853 MET cc_start: 0.8692 (mmm) cc_final: 0.8476 (mmp) REVERT: B 102 MET cc_start: 0.8011 (tpp) cc_final: 0.7238 (tpt) REVERT: C 106 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6078 (tp) REVERT: D 246 GLN cc_start: 0.6480 (tp40) cc_final: 0.6181 (tp-100) REVERT: E 119 GLN cc_start: 0.6286 (OUTLIER) cc_final: 0.5336 (pm20) REVERT: E 194 HIS cc_start: 0.6980 (OUTLIER) cc_final: 0.6766 (t-90) REVERT: E 343 TYR cc_start: 0.7893 (t80) cc_final: 0.7533 (t80) REVERT: F 1 MET cc_start: 0.4945 (ppp) cc_final: 0.4176 (ppp) REVERT: F 144 PHE cc_start: 0.8150 (t80) cc_final: 0.7583 (t80) REVERT: F 148 CYS cc_start: 0.7867 (m) cc_final: 0.7379 (m) REVERT: G 13 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7734 (mttp) REVERT: G 87 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.6899 (pp) outliers start: 122 outliers final: 95 residues processed: 402 average time/residue: 0.3446 time to fit residues: 210.2623 Evaluate side-chains 392 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 291 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 28 TRP Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 218 optimal weight: 0.9990 chunk 232 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 182 optimal weight: 20.0000 chunk 71 optimal weight: 0.6980 chunk 210 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 194 HIS E 213 HIS F 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21027 Z= 0.261 Angle : 0.667 12.049 28454 Z= 0.335 Chirality : 0.044 0.258 3317 Planarity : 0.005 0.073 3643 Dihedral : 7.348 119.416 2910 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.10 % Allowed : 21.86 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2601 helix: 0.54 (0.15), residues: 1234 sheet: -0.54 (0.23), residues: 493 loop : -0.93 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 307 HIS 0.024 0.001 HIS E 194 PHE 0.046 0.002 PHE F 215 TYR 0.027 0.002 TYR E 254 ARG 0.008 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 308 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7887 (m-80) REVERT: A 531 MET cc_start: 0.6944 (tpp) cc_final: 0.6498 (tpp) REVERT: A 655 ASN cc_start: 0.6828 (OUTLIER) cc_final: 0.6516 (m110) REVERT: A 853 MET cc_start: 0.8700 (mmm) cc_final: 0.8482 (mmp) REVERT: B 102 MET cc_start: 0.8028 (tpp) cc_final: 0.7255 (tpt) REVERT: B 229 MET cc_start: 0.7322 (tpp) cc_final: 0.6991 (tpp) REVERT: B 280 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7885 (ptpp) REVERT: C 106 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6122 (tp) REVERT: C 309 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6816 (tt0) REVERT: D 246 GLN cc_start: 0.6561 (tp40) cc_final: 0.6235 (tp-100) REVERT: E 119 GLN cc_start: 0.6319 (OUTLIER) cc_final: 0.5360 (pm20) REVERT: F 1 MET cc_start: 0.4956 (ppp) cc_final: 0.4193 (ppp) REVERT: F 144 PHE cc_start: 0.8180 (t80) cc_final: 0.7791 (t80) REVERT: G 13 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7740 (mttp) REVERT: G 87 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.6904 (pp) outliers start: 117 outliers final: 100 residues processed: 390 average time/residue: 0.3565 time to fit residues: 208.6833 Evaluate side-chains 400 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 293 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 81 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 chunk 258 optimal weight: 0.9990 chunk 237 optimal weight: 0.7980 chunk 205 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 213 HIS F 38 GLN G 36 ASN G 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21027 Z= 0.203 Angle : 0.662 12.065 28454 Z= 0.331 Chirality : 0.043 0.245 3317 Planarity : 0.004 0.075 3643 Dihedral : 7.212 119.504 2910 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.88 % Allowed : 23.30 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2601 helix: 0.66 (0.15), residues: 1234 sheet: -0.53 (0.24), residues: 487 loop : -0.83 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 307 HIS 0.006 0.001 HIS G 153 PHE 0.042 0.002 PHE F 215 TYR 0.022 0.001 TYR E 254 ARG 0.009 0.000 ARG C 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 302 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 MET cc_start: 0.6846 (tpp) cc_final: 0.6437 (tpp) REVERT: A 853 MET cc_start: 0.8683 (mmm) cc_final: 0.8466 (mmp) REVERT: B 102 MET cc_start: 0.8025 (tpp) cc_final: 0.7274 (tpt) REVERT: B 229 MET cc_start: 0.7241 (tpp) cc_final: 0.6987 (tpp) REVERT: C 106 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.5992 (tp) REVERT: C 309 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6757 (tt0) REVERT: D 246 GLN cc_start: 0.6441 (tp40) cc_final: 0.6218 (tp-100) REVERT: F 1 MET cc_start: 0.4897 (ppp) cc_final: 0.4121 (ppp) REVERT: F 144 PHE cc_start: 0.8176 (t80) cc_final: 0.7788 (t80) REVERT: G 13 LYS cc_start: 0.8124 (ttmm) cc_final: 0.7714 (mttp) REVERT: G 87 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.6836 (pp) outliers start: 89 outliers final: 79 residues processed: 364 average time/residue: 0.3461 time to fit residues: 188.6042 Evaluate side-chains 365 residues out of total 2293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 283 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 247 ASN Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 242 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 314 MET Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 24 ASN Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 162 CYS Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 189 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 26 optimal weight: 30.0000 chunk 37 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 ASN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 358 GLN E 194 HIS E 213 HIS ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN G 49 GLN H 177 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.186568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.150166 restraints weight = 34511.070| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.97 r_work: 0.3901 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21027 Z= 0.202 Angle : 0.654 12.107 28454 Z= 0.327 Chirality : 0.043 0.232 3317 Planarity : 0.004 0.074 3643 Dihedral : 7.097 118.812 2910 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.10 % Allowed : 23.25 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2601 helix: 0.74 (0.15), residues: 1237 sheet: -0.49 (0.24), residues: 486 loop : -0.83 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 28 HIS 0.005 0.001 HIS F 153 PHE 0.045 0.002 PHE E 339 TYR 0.023 0.001 TYR F 249 ARG 0.009 0.000 ARG C 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5068.63 seconds wall clock time: 91 minutes 46.06 seconds (5506.06 seconds total)