Starting phenix.real_space_refine on Sun Dec 10 16:47:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or4_17117/12_2023/8or4_17117.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or4_17117/12_2023/8or4_17117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or4_17117/12_2023/8or4_17117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or4_17117/12_2023/8or4_17117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or4_17117/12_2023/8or4_17117.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8or4_17117/12_2023/8or4_17117.pdb" } resolution = 3.8 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 85 5.16 5 C 9526 2.51 5 N 2557 2.21 5 O 2868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 18": "OD1" <-> "OD2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C ASP 213": "OD1" <-> "OD2" Residue "C TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 915": "OE1" <-> "OE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 134": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15036 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5231 Classifications: {'peptide': 656} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 11, 'TRANS': 644} Chain breaks: 7 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 9, 'PHE:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "B" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 311 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 6347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6347 Classifications: {'peptide': 843} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 37, 'TRANS': 805} Chain breaks: 11 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 7, 'ASP:plan': 4, 'PHE:plan': 2, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 127 Chain: "D" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 984 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain breaks: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1616 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 5 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 303 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 4, 'TRANS': 56} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 153 Chain: "H" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 244 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 5, 'TRANS': 43} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 111 Time building chain proxies: 8.41, per 1000 atoms: 0.56 Number of scatterers: 15036 At special positions: 0 Unit cell: (126.36, 179.28, 153.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 85 16.00 O 2868 8.00 N 2557 7.00 C 9526 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: 6.04 Conformation dependent library (CDL) restraints added in 3.0 seconds 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 4 sheets defined 66.0% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 removed outlier: 3.529A pdb=" N GLY A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.965A pdb=" N HIS A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 107 removed outlier: 3.636A pdb=" N ARG A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 137 removed outlier: 3.853A pdb=" N THR A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 159 through 172 removed outlier: 3.540A pdb=" N ASP A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 193 removed outlier: 3.993A pdb=" N GLN A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 211 Processing helix chain 'A' and resid 225 through 255 removed outlier: 5.382A pdb=" N SER A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLN A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 279 removed outlier: 3.953A pdb=" N MET A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN A 276 " --> pdb=" O GLN A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 283 through 296 removed outlier: 3.727A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 removed outlier: 4.091A pdb=" N GLN A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 332 through 356 removed outlier: 4.607A pdb=" N LEU A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 362 removed outlier: 3.762A pdb=" N LEU A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 385 Processing helix chain 'A' and resid 388 through 405 removed outlier: 3.833A pdb=" N ASN A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 removed outlier: 3.666A pdb=" N MET A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 removed outlier: 3.584A pdb=" N LEU A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 423 " --> pdb=" O PRO A 419 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 456 removed outlier: 3.941A pdb=" N TYR A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 476 removed outlier: 3.888A pdb=" N HIS A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 496 Processing helix chain 'A' and resid 497 through 528 removed outlier: 3.862A pdb=" N THR A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLN A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS A 522 " --> pdb=" O ASN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 removed outlier: 4.003A pdb=" N ARG A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N SER A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 Processing helix chain 'A' and resid 605 through 612 removed outlier: 3.695A pdb=" N LEU A 612 " --> pdb=" O MET A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 630 removed outlier: 4.098A pdb=" N ASP A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 628 " --> pdb=" O GLN A 624 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 629 " --> pdb=" O LEU A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 646 removed outlier: 3.523A pdb=" N SER A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 722 removed outlier: 3.864A pdb=" N GLN A 692 " --> pdb=" O MET A 688 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET A 721 " --> pdb=" O ARG A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 737 removed outlier: 3.699A pdb=" N LEU A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY A 732 " --> pdb=" O GLN A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 759 Processing helix chain 'B' and resid 80 through 92 removed outlier: 3.864A pdb=" N THR B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 16 removed outlier: 4.166A pdb=" N LEU C 11 " --> pdb=" O HIS C 7 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU C 12 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 36 removed outlier: 3.738A pdb=" N ARG C 23 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 57 Processing helix chain 'C' and resid 61 through 69 removed outlier: 3.940A pdb=" N GLN C 65 " --> pdb=" O ASN C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 removed outlier: 3.908A pdb=" N MET C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.563A pdb=" N SER C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 139 Processing helix chain 'C' and resid 140 through 143 Processing helix chain 'C' and resid 148 through 165 removed outlier: 3.848A pdb=" N LEU C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.546A pdb=" N VAL C 170 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASN C 171 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 181 removed outlier: 3.889A pdb=" N ILE C 176 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 186 removed outlier: 4.147A pdb=" N THR C 185 " --> pdb=" O PRO C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 206 removed outlier: 3.698A pdb=" N CYS C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 removed outlier: 3.930A pdb=" N GLU C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 245 removed outlier: 3.649A pdb=" N SER C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 265 removed outlier: 4.169A pdb=" N GLU C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) Proline residue: C 258 - end of helix removed outlier: 4.144A pdb=" N ASN C 265 " --> pdb=" O VAL C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 285 removed outlier: 3.702A pdb=" N CYS C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 303 removed outlier: 4.302A pdb=" N LYS C 303 " --> pdb=" O ASN C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 364 removed outlier: 4.021A pdb=" N ARG C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 383 removed outlier: 4.765A pdb=" N ALA C 378 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE C 383 " --> pdb=" O LEU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 406 removed outlier: 3.903A pdb=" N ALA C 392 " --> pdb=" O GLU C 388 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG C 406 " --> pdb=" O LEU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 443 removed outlier: 4.374A pdb=" N MET C 427 " --> pdb=" O THR C 423 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Proline residue: C 433 - end of helix removed outlier: 3.913A pdb=" N LYS C 441 " --> pdb=" O LYS C 437 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET C 443 " --> pdb=" O LEU C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 465 removed outlier: 4.044A pdb=" N ARG C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 486 Proline residue: C 478 - end of helix Processing helix chain 'C' and resid 490 through 507 removed outlier: 4.026A pdb=" N ASN C 507 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 515 No H-bonds generated for 'chain 'C' and resid 513 through 515' Processing helix chain 'C' and resid 516 through 528 Proline residue: C 522 - end of helix Processing helix chain 'C' and resid 532 through 549 removed outlier: 3.705A pdb=" N THR C 536 " --> pdb=" O PHE C 532 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU C 541 " --> pdb=" O SER C 537 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 542 " --> pdb=" O GLU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 577 removed outlier: 4.280A pdb=" N LYS C 566 " --> pdb=" O THR C 562 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASP C 567 " --> pdb=" O PRO C 563 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 568 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 601 Processing helix chain 'C' and resid 602 through 606 removed outlier: 3.538A pdb=" N GLY C 605 " --> pdb=" O ASP C 602 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER C 606 " --> pdb=" O ASN C 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 602 through 606' Processing helix chain 'C' and resid 607 through 621 removed outlier: 3.830A pdb=" N LYS C 620 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN C 621 " --> pdb=" O GLU C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 635 Processing helix chain 'C' and resid 644 through 650 Processing helix chain 'C' and resid 651 through 657 Processing helix chain 'C' and resid 666 through 677 removed outlier: 3.878A pdb=" N LEU C 671 " --> pdb=" O LYS C 667 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER C 672 " --> pdb=" O LEU C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.633A pdb=" N ALA C 687 " --> pdb=" O SER C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 removed outlier: 3.899A pdb=" N ASP C 695 " --> pdb=" O ASP C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 701 Proline residue: C 699 - end of helix No H-bonds generated for 'chain 'C' and resid 696 through 701' Processing helix chain 'C' and resid 702 through 720 removed outlier: 4.428A pdb=" N VAL C 708 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET C 711 " --> pdb=" O HIS C 707 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 718 " --> pdb=" O SER C 714 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 719 " --> pdb=" O PHE C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 743 Processing helix chain 'C' and resid 758 through 762 Processing helix chain 'C' and resid 763 through 768 Processing helix chain 'C' and resid 789 through 806 removed outlier: 3.591A pdb=" N SER C 795 " --> pdb=" O THR C 791 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 806 " --> pdb=" O CYS C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 813 Processing helix chain 'C' and resid 814 through 819 Processing helix chain 'C' and resid 827 through 836 removed outlier: 3.610A pdb=" N THR C 831 " --> pdb=" O ASN C 827 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 834 " --> pdb=" O SER C 830 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU C 836 " --> pdb=" O ASP C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 877 removed outlier: 4.280A pdb=" N ALA C 876 " --> pdb=" O VAL C 872 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER C 877 " --> pdb=" O LYS C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.667A pdb=" N ASN C 887 " --> pdb=" O SER C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 917 removed outlier: 3.836A pdb=" N LYS C 914 " --> pdb=" O LEU C 910 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 915 " --> pdb=" O HIS C 911 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 917 " --> pdb=" O LEU C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 933 removed outlier: 4.148A pdb=" N ILE C 932 " --> pdb=" O TYR C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 953 Processing helix chain 'D' and resid 20 through 23 Processing helix chain 'D' and resid 24 through 33 removed outlier: 4.501A pdb=" N MET D 30 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 31 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 62 through 67 removed outlier: 4.016A pdb=" N HIS D 65 " --> pdb=" O CYS D 62 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS D 66 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP D 67 " --> pdb=" O HIS D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 67' Processing helix chain 'D' and resid 92 through 100 removed outlier: 3.949A pdb=" N GLN D 96 " --> pdb=" O PRO D 92 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 98 " --> pdb=" O TRP D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 removed outlier: 3.928A pdb=" N GLU D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASN D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 134 Processing helix chain 'D' and resid 137 through 144 removed outlier: 4.748A pdb=" N ARG D 142 " --> pdb=" O GLU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'E' and resid 101 through 111 removed outlier: 3.851A pdb=" N LEU E 105 " --> pdb=" O PRO E 101 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 121 Processing helix chain 'E' and resid 124 through 132 removed outlier: 3.674A pdb=" N ARG E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU E 130 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER E 132 " --> pdb=" O TYR E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 159 removed outlier: 3.576A pdb=" N THR E 152 " --> pdb=" O HIS E 148 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 202 Processing helix chain 'E' and resid 219 through 229 removed outlier: 4.077A pdb=" N ILE E 222 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASN E 224 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 226 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS E 228 " --> pdb=" O THR E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 255 Processing helix chain 'G' and resid 25 through 32 removed outlier: 3.816A pdb=" N LYS G 30 " --> pdb=" O LYS G 26 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU G 31 " --> pdb=" O ASP G 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 188 Processing helix chain 'H' and resid 208 through 218 removed outlier: 4.064A pdb=" N ARG H 214 " --> pdb=" O ASP H 210 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ILE H 215 " --> pdb=" O GLN H 211 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 538 through 539 removed outlier: 6.299A pdb=" N GLN A 538 " --> pdb=" O ALA B 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.650A pdb=" N ILE D 4 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 16 " --> pdb=" O ILE D 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AA4, first strand: chain 'E' and resid 185 through 189 removed outlier: 3.570A pdb=" N SER E 212 " --> pdb=" O MET E 186 " (cutoff:3.500A) 729 hydrogen bonds defined for protein. 2121 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: 4.12 Time building geometry restraints manager: 6.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2721 1.33 - 1.45: 3439 1.45 - 1.57: 8954 1.57 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 15236 Sorted by residual: bond pdb=" CA GLN C 854 " pdb=" C GLN C 854 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.32e-02 5.74e+03 1.45e+01 bond pdb=" N GLN C 854 " pdb=" CA GLN C 854 " ideal model delta sigma weight residual 1.459 1.417 0.042 1.20e-02 6.94e+03 1.24e+01 bond pdb=" C GLN C 854 " pdb=" O GLN C 854 " ideal model delta sigma weight residual 1.236 1.202 0.035 1.15e-02 7.56e+03 9.02e+00 bond pdb=" CA GLN C 854 " pdb=" CB GLN C 854 " ideal model delta sigma weight residual 1.530 1.493 0.037 1.56e-02 4.11e+03 5.50e+00 bond pdb=" N GLU C 856 " pdb=" CA GLU C 856 " ideal model delta sigma weight residual 1.456 1.428 0.027 1.26e-02 6.30e+03 4.62e+00 ... (remaining 15231 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.27: 415 107.27 - 113.97: 8946 113.97 - 120.68: 6407 120.68 - 127.38: 4745 127.38 - 134.09: 126 Bond angle restraints: 20639 Sorted by residual: angle pdb=" N GLN C 854 " pdb=" CA GLN C 854 " pdb=" C GLN C 854 " ideal model delta sigma weight residual 111.11 117.41 -6.30 1.20e+00 6.94e-01 2.76e+01 angle pdb=" CA ARG E 415 " pdb=" CB ARG E 415 " pdb=" CG ARG E 415 " ideal model delta sigma weight residual 114.10 123.73 -9.63 2.00e+00 2.50e-01 2.32e+01 angle pdb=" N SER C 852 " pdb=" CA SER C 852 " pdb=" CB SER C 852 " ideal model delta sigma weight residual 110.65 103.74 6.91 1.58e+00 4.01e-01 1.91e+01 angle pdb=" N GLU C 856 " pdb=" CA GLU C 856 " pdb=" CB GLU C 856 " ideal model delta sigma weight residual 110.56 104.44 6.12 1.46e+00 4.69e-01 1.76e+01 angle pdb=" C SER C 852 " pdb=" CA SER C 852 " pdb=" CB SER C 852 " ideal model delta sigma weight residual 110.74 104.38 6.36 1.61e+00 3.86e-01 1.56e+01 ... (remaining 20634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8157 17.91 - 35.81: 906 35.81 - 53.72: 229 53.72 - 71.63: 37 71.63 - 89.53: 14 Dihedral angle restraints: 9343 sinusoidal: 3508 harmonic: 5835 Sorted by residual: dihedral pdb=" CA ARG C 664 " pdb=" C ARG C 664 " pdb=" N ALA C 665 " pdb=" CA ALA C 665 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA LEU C 925 " pdb=" C LEU C 925 " pdb=" N LYS C 926 " pdb=" CA LYS C 926 " ideal model delta harmonic sigma weight residual 180.00 155.68 24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" N SER C 852 " pdb=" C SER C 852 " pdb=" CA SER C 852 " pdb=" CB SER C 852 " ideal model delta harmonic sigma weight residual 122.80 112.77 10.03 0 2.50e+00 1.60e-01 1.61e+01 ... (remaining 9340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2364 0.071 - 0.143: 143 0.143 - 0.214: 0 0.214 - 0.285: 1 0.285 - 0.357: 4 Chirality restraints: 2512 Sorted by residual: chirality pdb=" CA ARG A 561 " pdb=" N ARG A 561 " pdb=" C ARG A 561 " pdb=" CB ARG A 561 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA ARG E 294 " pdb=" N ARG E 294 " pdb=" C ARG E 294 " pdb=" CB ARG E 294 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA GLN C 854 " pdb=" N GLN C 854 " pdb=" C GLN C 854 " pdb=" CB GLN C 854 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 2509 not shown) Planarity restraints: 2611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 625 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ARG C 625 " -0.075 2.00e-02 2.50e+03 pdb=" O ARG C 625 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU C 626 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 698 " 0.047 5.00e-02 4.00e+02 7.18e-02 8.25e+00 pdb=" N PRO C 699 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 699 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 699 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 853 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C GLY C 853 " -0.042 2.00e-02 2.50e+03 pdb=" O GLY C 853 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN C 854 " 0.014 2.00e-02 2.50e+03 ... (remaining 2608 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 122 2.52 - 3.12: 12505 3.12 - 3.71: 22644 3.71 - 4.31: 28014 4.31 - 4.90: 46238 Nonbonded interactions: 109523 Sorted by model distance: nonbonded pdb=" O LYS C 914 " pdb=" OG SER C 918 " model vdw 1.930 2.440 nonbonded pdb=" OH TYR C 372 " pdb=" OG1 THR C 405 " model vdw 1.994 2.440 nonbonded pdb=" OD2 ASP A 427 " pdb=" CG MET A 469 " model vdw 2.012 3.440 nonbonded pdb=" NZ LYS C 667 " pdb=" OD1 ASP C 705 " model vdw 2.017 2.520 nonbonded pdb=" O PHE C 371 " pdb=" OG1 THR C 374 " model vdw 2.019 2.440 ... (remaining 109518 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.650 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: 0.020 Extract box with map and model: 7.400 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 41.510 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 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 : 0.003 0.050 15236 Z= 0.176 Angle : 0.588 9.639 20639 Z= 0.307 Chirality : 0.037 0.357 2512 Planarity : 0.004 0.072 2611 Dihedral : 16.205 89.532 5503 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.31 % Allowed : 24.89 % Favored : 74.80 % Cbeta Deviations : 0.05 % 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: 0.05 (0.21), residues: 1914 helix: 1.35 (0.17), residues: 1026 sheet: 0.42 (1.35), residues: 21 loop : -1.68 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 123 HIS 0.002 0.000 HIS A 343 PHE 0.020 0.001 PHE A 402 TYR 0.012 0.001 TYR A 99 ARG 0.007 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 355 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 359 average time/residue: 0.2668 time to fit residues: 140.6415 Evaluate side-chains 336 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 334 time to evaluate : 1.828 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1388 time to fit residues: 3.3634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 0.0470 chunk 100 optimal weight: 0.0570 chunk 79 optimal weight: 0.4980 chunk 153 optimal weight: 0.0770 chunk 59 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 177 optimal weight: 0.7980 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 HIS A 700 HIS C 299 ASN C 514 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15236 Z= 0.195 Angle : 0.653 11.234 20639 Z= 0.323 Chirality : 0.039 0.201 2512 Planarity : 0.004 0.063 2611 Dihedral : 4.124 24.686 2057 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.93 % Allowed : 22.83 % Favored : 73.24 % 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: -0.03 (0.20), residues: 1914 helix: 1.22 (0.16), residues: 1073 sheet: 2.81 (1.41), residues: 11 loop : -1.80 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 410 HIS 0.005 0.001 HIS C 173 PHE 0.028 0.001 PHE A 498 TYR 0.013 0.001 TYR A 278 ARG 0.009 0.001 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 365 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 34 residues processed: 394 average time/residue: 0.2654 time to fit residues: 153.8556 Evaluate side-chains 372 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 338 time to evaluate : 1.833 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1635 time to fit residues: 12.0206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.0970 chunk 55 optimal weight: 4.9990 chunk 148 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 178 optimal weight: 0.5980 chunk 192 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 284 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 GLN A 700 HIS C 201 HIS C 299 ASN D 49 ASN D 65 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15236 Z= 0.205 Angle : 0.665 12.313 20639 Z= 0.324 Chirality : 0.040 0.163 2512 Planarity : 0.004 0.056 2611 Dihedral : 4.249 22.693 2057 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.06 % Allowed : 24.14 % Favored : 72.80 % 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: -0.17 (0.20), residues: 1914 helix: 1.11 (0.16), residues: 1079 sheet: None (None), residues: 0 loop : -1.82 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 410 HIS 0.004 0.001 HIS C 173 PHE 0.025 0.001 PHE A 402 TYR 0.022 0.001 TYR A 260 ARG 0.009 0.001 ARG E 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 363 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 15 residues processed: 400 average time/residue: 0.2634 time to fit residues: 155.4766 Evaluate side-chains 364 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 349 time to evaluate : 1.616 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1327 time to fit residues: 6.0675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 0.5980 chunk 189 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 505 GLN A 641 GLN A 700 HIS C 299 ASN D 49 ASN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15236 Z= 0.249 Angle : 0.704 12.564 20639 Z= 0.347 Chirality : 0.041 0.227 2512 Planarity : 0.004 0.055 2611 Dihedral : 4.599 23.514 2057 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.81 % Allowed : 26.64 % Favored : 69.56 % 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: -0.50 (0.20), residues: 1914 helix: 0.79 (0.16), residues: 1091 sheet: -3.92 (1.02), residues: 10 loop : -1.88 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 144 HIS 0.008 0.001 HIS C 508 PHE 0.024 0.002 PHE A 402 TYR 0.019 0.002 TYR A 260 ARG 0.009 0.001 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 374 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 32 residues processed: 406 average time/residue: 0.2791 time to fit residues: 167.0771 Evaluate side-chains 386 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 354 time to evaluate : 1.774 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1672 time to fit residues: 12.0038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.0980 chunk 107 optimal weight: 0.8980 chunk 2 optimal weight: 0.0870 chunk 141 optimal weight: 0.6980 chunk 78 optimal weight: 0.0970 chunk 161 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 47 optimal weight: 0.0570 overall best weight: 0.1874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 368 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 524 HIS A 641 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15236 Z= 0.176 Angle : 0.697 12.667 20639 Z= 0.332 Chirality : 0.040 0.166 2512 Planarity : 0.004 0.056 2611 Dihedral : 4.325 22.744 2057 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.31 % Allowed : 28.57 % Favored : 69.12 % 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: -0.29 (0.20), residues: 1914 helix: 0.98 (0.16), residues: 1086 sheet: -3.69 (1.16), residues: 10 loop : -1.81 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 123 HIS 0.011 0.001 HIS A 343 PHE 0.021 0.001 PHE A 402 TYR 0.029 0.001 TYR A 260 ARG 0.008 0.001 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 370 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 18 residues processed: 391 average time/residue: 0.2725 time to fit residues: 155.5696 Evaluate side-chains 369 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 351 time to evaluate : 1.729 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1860 time to fit residues: 7.8202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.0270 chunk 170 optimal weight: 0.0370 chunk 37 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 189 optimal weight: 10.0000 chunk 157 optimal weight: 0.0020 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 99 optimal weight: 0.0270 overall best weight: 0.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 641 GLN A 700 HIS C 265 ASN C 299 ASN C 663 GLN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15236 Z= 0.175 Angle : 0.687 14.210 20639 Z= 0.329 Chirality : 0.039 0.161 2512 Planarity : 0.004 0.059 2611 Dihedral : 4.228 21.795 2057 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.06 % Allowed : 29.82 % Favored : 68.12 % 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: -0.27 (0.20), residues: 1914 helix: 0.98 (0.16), residues: 1080 sheet: -3.47 (1.26), residues: 10 loop : -1.76 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 123 HIS 0.009 0.001 HIS A 343 PHE 0.024 0.001 PHE C 482 TYR 0.023 0.001 TYR A 260 ARG 0.008 0.001 ARG E 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 369 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 15 residues processed: 386 average time/residue: 0.2720 time to fit residues: 153.8947 Evaluate side-chains 374 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 359 time to evaluate : 1.790 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1592 time to fit residues: 6.4935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.0170 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 188 optimal weight: 0.1980 chunk 118 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN A 368 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN A 641 GLN A 700 HIS C 265 ASN C 299 ASN D 65 HIS ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15236 Z= 0.195 Angle : 0.695 14.715 20639 Z= 0.332 Chirality : 0.039 0.177 2512 Planarity : 0.004 0.059 2611 Dihedral : 4.243 22.282 2057 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.06 % Allowed : 31.13 % Favored : 67.81 % 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: -0.27 (0.20), residues: 1914 helix: 0.96 (0.16), residues: 1090 sheet: -0.24 (1.22), residues: 20 loop : -1.83 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 123 HIS 0.006 0.001 HIS A 343 PHE 0.047 0.001 PHE A 498 TYR 0.042 0.001 TYR A 260 ARG 0.008 0.000 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 371 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 379 average time/residue: 0.2780 time to fit residues: 153.8473 Evaluate side-chains 367 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 359 time to evaluate : 1.702 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1462 time to fit residues: 4.5689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 112 optimal weight: 0.0970 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 0.0060 chunk 36 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 chunk 128 optimal weight: 0.4980 chunk 93 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 284 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 641 GLN A 700 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN C 299 ASN D 65 HIS D 96 GLN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15236 Z= 0.193 Angle : 0.715 15.662 20639 Z= 0.339 Chirality : 0.040 0.220 2512 Planarity : 0.004 0.060 2611 Dihedral : 4.215 22.213 2057 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.31 % Allowed : 31.88 % Favored : 66.81 % 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: -0.30 (0.20), residues: 1914 helix: 0.93 (0.16), residues: 1084 sheet: -0.27 (1.24), residues: 20 loop : -1.81 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 123 HIS 0.007 0.001 HIS A 343 PHE 0.033 0.001 PHE A 498 TYR 0.034 0.001 TYR A 260 ARG 0.008 0.000 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 368 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 375 average time/residue: 0.2778 time to fit residues: 152.0029 Evaluate side-chains 368 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 357 time to evaluate : 1.685 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1623 time to fit residues: 5.5423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 2.9990 chunk 180 optimal weight: 0.0670 chunk 165 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 166 optimal weight: 0.2980 chunk 175 optimal weight: 0.2980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN A 368 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 641 GLN A 700 HIS C 265 ASN C 299 ASN D 65 HIS ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15236 Z= 0.199 Angle : 0.721 16.767 20639 Z= 0.344 Chirality : 0.040 0.194 2512 Planarity : 0.004 0.074 2611 Dihedral : 4.275 23.047 2057 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.81 % Allowed : 31.75 % Favored : 67.44 % 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: -0.34 (0.20), residues: 1914 helix: 0.88 (0.16), residues: 1083 sheet: -0.18 (1.18), residues: 20 loop : -1.79 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 123 HIS 0.006 0.001 HIS A 343 PHE 0.029 0.001 PHE A 498 TYR 0.041 0.001 TYR A 260 ARG 0.007 0.000 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 366 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 371 average time/residue: 0.2742 time to fit residues: 149.0140 Evaluate side-chains 362 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 355 time to evaluate : 1.800 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1459 time to fit residues: 4.2305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 113 optimal weight: 0.0010 chunk 88 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 195 optimal weight: 0.0770 chunk 179 optimal weight: 0.3980 chunk 155 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 95 optimal weight: 0.2980 overall best weight: 0.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 641 GLN A 700 HIS C 265 ASN ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15236 Z= 0.187 Angle : 0.721 17.939 20639 Z= 0.345 Chirality : 0.040 0.223 2512 Planarity : 0.004 0.078 2611 Dihedral : 4.199 22.663 2057 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.37 % Allowed : 32.94 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1914 helix: 0.87 (0.16), residues: 1083 sheet: -0.12 (1.20), residues: 20 loop : -1.77 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 123 HIS 0.006 0.001 HIS A 343 PHE 0.029 0.001 PHE A 498 TYR 0.039 0.001 TYR A 260 ARG 0.007 0.000 ARG C 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 365 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 367 average time/residue: 0.2847 time to fit residues: 152.4237 Evaluate side-chains 356 residues out of total 1803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 355 time to evaluate : 1.839 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1354 time to fit residues: 2.8763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.4980 chunk 165 optimal weight: 0.0370 chunk 47 optimal weight: 0.0670 chunk 143 optimal weight: 0.0050 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 155 optimal weight: 0.0270 chunk 65 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.1268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 GLN A 700 HIS C 265 ASN D 65 HIS ** E 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.157689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.133934 restraints weight = 30799.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.138087 restraints weight = 17303.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.140952 restraints weight = 11024.586| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15236 Z= 0.192 Angle : 0.728 18.082 20639 Z= 0.348 Chirality : 0.040 0.355 2512 Planarity : 0.004 0.075 2611 Dihedral : 4.153 21.668 2057 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.56 % Allowed : 32.88 % Favored : 66.56 % 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: -0.28 (0.20), residues: 1914 helix: 0.89 (0.16), residues: 1077 sheet: 0.04 (1.12), residues: 22 loop : -1.72 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 123 HIS 0.006 0.001 HIS A 343 PHE 0.031 0.001 PHE A 498 TYR 0.020 0.001 TYR A 323 ARG 0.007 0.000 ARG C 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3698.80 seconds wall clock time: 67 minutes 44.55 seconds (4064.55 seconds total)