Starting phenix.real_space_refine on Fri Feb 16 16:16:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr7_22443/02_2024/7jr7_22443.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr7_22443/02_2024/7jr7_22443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr7_22443/02_2024/7jr7_22443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr7_22443/02_2024/7jr7_22443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr7_22443/02_2024/7jr7_22443.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr7_22443/02_2024/7jr7_22443.pdb" } resolution = 3.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 10115 2.51 5 N 2657 2.21 5 O 2940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 34": "OE1" <-> "OE2" Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 286": "OD1" <-> "OD2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 450": "OD1" <-> "OD2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "B PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B ASP 636": "OD1" <-> "OD2" Residue "B TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1": "OD1" <-> "OD2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 152": "OD1" <-> "OD2" Residue "D ASP 166": "OD1" <-> "OD2" Residue "D ASP 185": "OD1" <-> "OD2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 73": "OD1" <-> "OD2" Residue "E TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 182": "OD1" <-> "OD2" Residue "E ASP 223": "OD1" <-> "OD2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F ASP 143": "OD1" <-> "OD2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 187": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15799 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4626 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 22, 'TRANS': 565} Chain breaks: 2 Chain: "B" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4609 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 24, 'TRANS': 554} Chain breaks: 3 Chain: "C" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1638 Classifications: {'peptide': 210} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 194} Chain breaks: 1 Chain: "D" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1627 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "E" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1663 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Chain: "F" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1636 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 202} Time building chain proxies: 10.23, per 1000 atoms: 0.65 Number of scatterers: 15799 At special positions: 0 Unit cell: (158.82, 158.82, 130.232, 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 87 16.00 O 2940 8.00 N 2657 7.00 C 10115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 149 " - pdb=" SG CYS E 204 " distance=2.05 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.04 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: 6.45 Conformation dependent library (CDL) restraints added in 3.7 seconds 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3772 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 25 sheets defined 40.0% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 121 through 127 removed outlier: 4.604A pdb=" N GLN A 126 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 161 through 175 removed outlier: 3.565A pdb=" N GLN A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 removed outlier: 3.623A pdb=" N GLY A 192 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 208 Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.807A pdb=" N GLN A 258 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 311 through 331 removed outlier: 3.588A pdb=" N LYS A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 347 removed outlier: 3.678A pdb=" N LYS A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 381 Processing helix chain 'A' and resid 382 through 404 removed outlier: 5.443A pdb=" N ASN A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 455 Proline residue: A 431 - end of helix Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 459 through 471 removed outlier: 3.768A pdb=" N MET A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 471 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 491 removed outlier: 3.705A pdb=" N VAL A 485 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TRP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 522 Proline residue: A 509 - end of helix Processing helix chain 'A' and resid 526 through 546 removed outlier: 3.515A pdb=" N VAL A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 removed outlier: 4.014A pdb=" N MET A 555 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 566 through 581 removed outlier: 4.218A pdb=" N TYR A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.630A pdb=" N PHE A 608 " --> pdb=" O GLN A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 618 Processing helix chain 'A' and resid 619 through 628 Processing helix chain 'A' and resid 629 through 646 removed outlier: 3.573A pdb=" N ALA A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 180 through 195 Processing helix chain 'B' and resid 214 through 228 removed outlier: 4.226A pdb=" N GLN B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 261 Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 316 through 326 Processing helix chain 'B' and resid 331 through 353 Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.583A pdb=" N PHE B 359 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 360 " --> pdb=" O ASP B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 356 through 360' Processing helix chain 'B' and resid 394 through 411 Processing helix chain 'B' and resid 413 through 435 removed outlier: 3.514A pdb=" N LEU B 417 " --> pdb=" O ASP B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 458 Processing helix chain 'B' and resid 459 through 474 removed outlier: 3.814A pdb=" N VAL B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 485 Processing helix chain 'B' and resid 488 through 499 removed outlier: 3.626A pdb=" N TYR B 492 " --> pdb=" O THR B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 519 removed outlier: 4.048A pdb=" N ALA B 506 " --> pdb=" O PRO B 502 " (cutoff:3.500A) Proline residue: B 514 - end of helix Processing helix chain 'B' and resid 524 through 551 removed outlier: 3.586A pdb=" N PHE B 528 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 573 Processing helix chain 'B' and resid 584 through 593 removed outlier: 3.719A pdb=" N VAL B 593 " --> pdb=" O TRP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 608 Processing helix chain 'B' and resid 625 through 633 Processing helix chain 'B' and resid 639 through 665 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.582A pdb=" N THR C 91 " --> pdb=" O THR C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.795A pdb=" N ALA D 84 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 184 through 188 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.520A pdb=" N ARG E 65 " --> pdb=" O GLU E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 209 through 212 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 77 removed outlier: 6.660A pdb=" N GLU A 112 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69 removed outlier: 6.123A pdb=" N TYR A 45 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 132 removed outlier: 6.197A pdb=" N MET A 82 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 263 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N CYS A 274 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE A 265 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 88 through 96 removed outlier: 3.647A pdb=" N ASN B 90 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU B 52 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER B 92 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG B 50 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS B 94 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU B 48 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG B 96 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR B 46 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU B 52 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER B 129 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR B 54 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE B 127 " --> pdb=" O TYR B 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.479A pdb=" N LEU B 101 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 283 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 294 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU B 285 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.531A pdb=" N SER C 69 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.644A pdb=" N TRP C 37 " --> pdb=" O MET C 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.973A pdb=" N CYS C 96 " --> pdb=" O TRP C 109 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP C 109 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG C 98 " --> pdb=" O ASP C 107 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C 105 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 126 through 130 removed outlier: 6.027A pdb=" N TYR C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N SER C 184 " --> pdb=" O PRO C 173 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER C 186 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N THR C 171 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 157 through 160 Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.372A pdb=" N THR D 70 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N SER D 27 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 10.742A pdb=" N SER D 68 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N ALA D 29 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 11.853A pdb=" N SER D 66 " --> pdb=" O ALA D 29 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 13 removed outlier: 5.682A pdb=" N GLN D 38 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU D 47 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AB5, first strand: chain 'D' and resid 115 through 119 removed outlier: 4.840A pdb=" N SER D 132 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU D 182 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL D 134 " --> pdb=" O ALA D 180 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA D 180 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE D 136 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER D 178 " --> pdb=" O PHE D 136 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN D 138 " --> pdb=" O MET D 176 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET D 176 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.489A pdb=" N ILE E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AC1, first strand: chain 'E' and resid 129 through 133 removed outlier: 4.346A pdb=" N GLY E 148 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 145 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR E 184 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER E 187 " --> pdb=" O PRO E 176 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N SER E 189 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR E 174 " --> pdb=" O SER E 189 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR E 191 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL E 172 " --> pdb=" O THR E 191 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 160 through 163 Processing sheet with id=AC3, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.417A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.928A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 114 through 118 removed outlier: 4.730A pdb=" N SER F 131 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU F 181 " --> pdb=" O SER F 131 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL F 133 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU F 179 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N PHE F 135 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER F 177 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN F 137 " --> pdb=" O MET F 175 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET F 175 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 153 through 154 830 hydrogen bonds defined for protein. 2271 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 6.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4790 1.34 - 1.47: 4216 1.47 - 1.59: 7029 1.59 - 1.72: 0 1.72 - 1.84: 136 Bond restraints: 16171 Sorted by residual: bond pdb=" CG LEU E 37 " pdb=" CD1 LEU E 37 " ideal model delta sigma weight residual 1.521 1.423 0.098 3.30e-02 9.18e+02 8.82e+00 bond pdb=" CG1 ILE B 403 " pdb=" CD1 ILE B 403 " ideal model delta sigma weight residual 1.513 1.403 0.110 3.90e-02 6.57e+02 7.93e+00 bond pdb=" C ILE B 459 " pdb=" N PRO B 460 " ideal model delta sigma weight residual 1.333 1.373 -0.039 1.44e-02 4.82e+03 7.48e+00 bond pdb=" C PHE A 442 " pdb=" N PRO A 443 " ideal model delta sigma weight residual 1.333 1.370 -0.037 1.44e-02 4.82e+03 6.63e+00 bond pdb=" CG LEU B 486 " pdb=" CD2 LEU B 486 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.12e+00 ... (remaining 16166 not shown) Histogram of bond angle deviations from ideal: 96.85 - 105.24: 374 105.24 - 113.63: 8870 113.63 - 122.02: 9408 122.02 - 130.41: 3203 130.41 - 138.80: 104 Bond angle restraints: 21959 Sorted by residual: angle pdb=" N GLY E 104 " pdb=" CA GLY E 104 " pdb=" C GLY E 104 " ideal model delta sigma weight residual 112.34 128.50 -16.16 2.04e+00 2.40e-01 6.27e+01 angle pdb=" C ARG F 211 " pdb=" N ALA F 212 " pdb=" CA ALA F 212 " ideal model delta sigma weight residual 121.70 135.22 -13.52 1.80e+00 3.09e-01 5.64e+01 angle pdb=" C ARG C 76 " pdb=" N ASN C 77 " pdb=" CA ASN C 77 " ideal model delta sigma weight residual 122.74 133.50 -10.76 1.44e+00 4.82e-01 5.58e+01 angle pdb=" C THR B 287 " pdb=" N SER B 288 " pdb=" CA SER B 288 " ideal model delta sigma weight residual 120.81 132.74 -11.93 1.63e+00 3.76e-01 5.36e+01 angle pdb=" CA CYS F 134 " pdb=" CB CYS F 134 " pdb=" SG CYS F 134 " ideal model delta sigma weight residual 114.40 129.93 -15.53 2.30e+00 1.89e-01 4.56e+01 ... (remaining 21954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 9075 17.64 - 35.28: 411 35.28 - 52.92: 104 52.92 - 70.55: 28 70.55 - 88.19: 12 Dihedral angle restraints: 9630 sinusoidal: 3763 harmonic: 5867 Sorted by residual: dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 195 " pdb=" CB CYS D 195 " ideal model delta sinusoidal sigma weight residual 93.00 170.39 -77.39 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS F 134 " pdb=" SG CYS F 134 " pdb=" SG CYS F 194 " pdb=" CB CYS F 194 " ideal model delta sinusoidal sigma weight residual 93.00 159.01 -66.01 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" C ILE B 459 " pdb=" N ILE B 459 " pdb=" CA ILE B 459 " pdb=" CB ILE B 459 " ideal model delta harmonic sigma weight residual -122.00 -133.10 11.10 0 2.50e+00 1.60e-01 1.97e+01 ... (remaining 9627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2208 0.112 - 0.225: 264 0.225 - 0.337: 30 0.337 - 0.450: 0 0.450 - 0.562: 1 Chirality restraints: 2503 Sorted by residual: chirality pdb=" CG LEU D 34 " pdb=" CB LEU D 34 " pdb=" CD1 LEU D 34 " pdb=" CD2 LEU D 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" CB ILE A 81 " pdb=" CA ILE A 81 " pdb=" CG1 ILE A 81 " pdb=" CG2 ILE A 81 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB ILE B 235 " pdb=" CA ILE B 235 " pdb=" CG1 ILE B 235 " pdb=" CG2 ILE B 235 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2500 not shown) Planarity restraints: 2763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 189 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C VAL C 189 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL C 189 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO C 190 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 617 " 0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C THR A 617 " -0.058 2.00e-02 2.50e+03 pdb=" O THR A 617 " 0.022 2.00e-02 2.50e+03 pdb=" N SER A 618 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 49 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C SER F 49 " 0.057 2.00e-02 2.50e+03 pdb=" O SER F 49 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA F 50 " -0.020 2.00e-02 2.50e+03 ... (remaining 2760 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3170 2.78 - 3.31: 14434 3.31 - 3.84: 26231 3.84 - 4.37: 29867 4.37 - 4.90: 53606 Nonbonded interactions: 127308 Sorted by model distance: nonbonded pdb=" OG SER D 122 " pdb=" OE1 GLU D 124 " model vdw 2.254 2.440 nonbonded pdb=" OG1 THR B 287 " pdb=" O THR B 325 " model vdw 2.258 2.440 nonbonded pdb=" NZ LYS B 605 " pdb=" O TYR B 638 " model vdw 2.266 2.520 nonbonded pdb=" NH1 ARG B 164 " pdb=" OE2 GLU B 189 " model vdw 2.267 2.520 nonbonded pdb=" O GLY C 163 " pdb=" OG SER C 166 " model vdw 2.268 2.440 ... (remaining 127303 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=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: 2.880 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: 0.010 Extract box with map and model: 12.190 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 47.380 Find NCS groups from input model: 0.540 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.010 0.110 16171 Z= 0.635 Angle : 1.338 16.156 21959 Z= 0.748 Chirality : 0.076 0.562 2503 Planarity : 0.008 0.041 2763 Dihedral : 11.829 88.193 5831 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.40 % Allowed : 2.56 % Favored : 97.04 % Rotamer: Outliers : 0.57 % Allowed : 4.99 % Favored : 94.44 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 11.46 % 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: 0.62 (0.18), residues: 1994 helix: 0.78 (0.18), residues: 727 sheet: 0.76 (0.23), residues: 475 loop : -0.00 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP B 229 HIS 0.012 0.003 HIS E 57 PHE 0.054 0.005 PHE C 83 TYR 0.049 0.005 TYR B 472 ARG 0.013 0.002 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 327 time to evaluate : 1.880 Fit side-chains REVERT: A 413 LYS cc_start: 0.7925 (mmtt) cc_final: 0.7282 (tppt) REVERT: A 480 MET cc_start: 0.7756 (mmm) cc_final: 0.7367 (mmt) REVERT: B 89 GLN cc_start: 0.6824 (mt0) cc_final: 0.6533 (mt0) REVERT: B 413 ASP cc_start: 0.7893 (t0) cc_final: 0.7625 (t70) REVERT: E 183 LEU cc_start: 0.8402 (mp) cc_final: 0.8012 (mm) REVERT: F 15 LEU cc_start: 0.8097 (tt) cc_final: 0.7539 (mp) outliers start: 10 outliers final: 5 residues processed: 336 average time/residue: 0.3179 time to fit residues: 151.2575 Evaluate side-chains 201 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 196 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain F residue 181 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 0.7980 chunk 150 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 155 optimal weight: 40.0000 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 310 GLN A 392 GLN A 393 ASN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN A 551 ASN A 578 ASN B 55 GLN B 89 GLN B 250 ASN B 299 HIS C 78 GLN D 54 ASN E 5 GLN E 43 HIS ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN F 166 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16171 Z= 0.230 Angle : 0.651 10.294 21959 Z= 0.347 Chirality : 0.045 0.215 2503 Planarity : 0.005 0.109 2763 Dihedral : 4.896 34.360 2198 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.51 % Favored : 97.39 % Rotamer: Outliers : 2.38 % Allowed : 9.47 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.06 (0.19), residues: 1994 helix: 1.50 (0.19), residues: 737 sheet: 0.89 (0.23), residues: 497 loop : -0.13 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 229 HIS 0.005 0.001 HIS B 504 PHE 0.026 0.002 PHE A 608 TYR 0.032 0.002 TYR B 472 ARG 0.012 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 205 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 452 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7768 (mt-10) REVERT: A 480 MET cc_start: 0.7837 (mmm) cc_final: 0.7240 (mmt) REVERT: B 89 GLN cc_start: 0.7177 (mt0) cc_final: 0.6857 (mt0) REVERT: B 615 MET cc_start: 0.5548 (tmm) cc_final: 0.4991 (ttp) REVERT: B 668 LYS cc_start: 0.8294 (mttm) cc_final: 0.8021 (mtmm) REVERT: D 195 CYS cc_start: 0.2482 (m) cc_final: 0.2091 (m) REVERT: F 15 LEU cc_start: 0.8254 (tt) cc_final: 0.7549 (mp) outliers start: 42 outliers final: 22 residues processed: 235 average time/residue: 0.2728 time to fit residues: 96.0509 Evaluate side-chains 205 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 123 optimal weight: 0.0870 chunk 49 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN B 153 GLN B 504 HIS B 526 GLN C 202 ASN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN F 210 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16171 Z= 0.285 Angle : 0.641 10.012 21959 Z= 0.337 Chirality : 0.044 0.184 2503 Planarity : 0.005 0.050 2763 Dihedral : 4.667 37.950 2192 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.41 % Favored : 96.49 % Rotamer: Outliers : 2.89 % Allowed : 10.83 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.96 (0.19), residues: 1994 helix: 1.43 (0.19), residues: 740 sheet: 0.89 (0.23), residues: 499 loop : -0.26 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 109 HIS 0.008 0.001 HIS B 150 PHE 0.021 0.002 PHE B 493 TYR 0.028 0.002 TYR B 472 ARG 0.005 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 200 time to evaluate : 1.866 Fit side-chains revert: symmetry clash REVERT: A 452 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7842 (mt-10) REVERT: A 470 HIS cc_start: 0.9019 (OUTLIER) cc_final: 0.8711 (p90) REVERT: A 480 MET cc_start: 0.7933 (mmm) cc_final: 0.7254 (mmt) REVERT: B 121 ARG cc_start: 0.8292 (ptp-170) cc_final: 0.8045 (mtt180) REVERT: B 668 LYS cc_start: 0.8488 (mttm) cc_final: 0.8216 (mtmt) REVERT: C 89 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: F 15 LEU cc_start: 0.8278 (tt) cc_final: 0.7518 (mp) outliers start: 51 outliers final: 35 residues processed: 232 average time/residue: 0.2918 time to fit residues: 104.3921 Evaluate side-chains 218 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 181 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 7.9990 chunk 136 optimal weight: 0.0170 chunk 93 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 121 optimal weight: 0.2980 chunk 181 optimal weight: 0.6980 chunk 192 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 ASN C 5 GLN E 57 HIS F 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16171 Z= 0.156 Angle : 0.565 8.194 21959 Z= 0.294 Chirality : 0.042 0.182 2503 Planarity : 0.004 0.042 2763 Dihedral : 4.421 36.716 2192 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.11 % Favored : 96.79 % Rotamer: Outliers : 2.61 % Allowed : 12.37 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.13 (0.19), residues: 1994 helix: 1.70 (0.19), residues: 742 sheet: 0.95 (0.23), residues: 498 loop : -0.28 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 584 HIS 0.006 0.001 HIS B 438 PHE 0.019 0.001 PHE A 608 TYR 0.024 0.001 TYR E 107 ARG 0.005 0.000 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 195 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 452 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7795 (mt-10) REVERT: A 470 HIS cc_start: 0.8940 (OUTLIER) cc_final: 0.8595 (p90) REVERT: A 480 MET cc_start: 0.7959 (mmm) cc_final: 0.7421 (mmt) REVERT: A 579 GLU cc_start: 0.7712 (tp30) cc_final: 0.7440 (tp30) REVERT: A 622 MET cc_start: 0.7307 (tpt) cc_final: 0.6899 (tpt) REVERT: B 269 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8595 (tt) REVERT: B 615 MET cc_start: 0.5757 (tmm) cc_final: 0.5185 (ttp) REVERT: B 668 LYS cc_start: 0.8485 (mttm) cc_final: 0.8209 (mtmt) REVERT: C 89 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: E 180 GLN cc_start: 0.7498 (pm20) cc_final: 0.7297 (pm20) outliers start: 46 outliers final: 27 residues processed: 227 average time/residue: 0.2752 time to fit residues: 93.4960 Evaluate side-chains 209 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 179 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 0 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS A 578 ASN E 84 ASN F 89 GLN F 166 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16171 Z= 0.390 Angle : 0.669 9.679 21959 Z= 0.348 Chirality : 0.046 0.194 2503 Planarity : 0.005 0.053 2763 Dihedral : 4.792 42.722 2192 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 3.80 % Allowed : 11.97 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.80 (0.19), residues: 1994 helix: 1.31 (0.19), residues: 738 sheet: 0.92 (0.23), residues: 499 loop : -0.46 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 163 HIS 0.008 0.001 HIS B 150 PHE 0.024 0.002 PHE B 493 TYR 0.028 0.002 TYR B 472 ARG 0.006 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 190 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.8333 (tpp) cc_final: 0.8128 (tpp) REVERT: A 452 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7904 (mt-10) REVERT: A 480 MET cc_start: 0.7935 (mmm) cc_final: 0.7475 (mmt) REVERT: B 220 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7451 (mtm180) REVERT: B 668 LYS cc_start: 0.8605 (mttm) cc_final: 0.8330 (mtmt) REVERT: C 36 ASN cc_start: 0.9253 (OUTLIER) cc_final: 0.9014 (p0) REVERT: C 89 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: E 180 GLN cc_start: 0.7615 (pm20) cc_final: 0.7386 (pm20) REVERT: E 185 THR cc_start: 0.8444 (p) cc_final: 0.8198 (p) REVERT: F 170 ASP cc_start: 0.8393 (t0) cc_final: 0.7855 (t0) outliers start: 67 outliers final: 50 residues processed: 238 average time/residue: 0.2685 time to fit residues: 97.3109 Evaluate side-chains 238 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 186 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 0.5980 chunk 173 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 159 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS A 578 ASN B 462 ASN F 166 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16171 Z= 0.156 Angle : 0.559 9.545 21959 Z= 0.290 Chirality : 0.041 0.181 2503 Planarity : 0.004 0.043 2763 Dihedral : 4.471 39.995 2192 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 2.33 % Allowed : 13.61 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.07 (0.19), residues: 1994 helix: 1.72 (0.19), residues: 741 sheet: 1.01 (0.23), residues: 496 loop : -0.49 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 584 HIS 0.004 0.001 HIS F 189 PHE 0.016 0.001 PHE A 608 TYR 0.019 0.001 TYR B 571 ARG 0.003 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 1.939 Fit side-chains revert: symmetry clash REVERT: A 452 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7787 (mt-10) REVERT: A 480 MET cc_start: 0.7917 (mmm) cc_final: 0.7355 (mmt) REVERT: B 615 MET cc_start: 0.5814 (tmm) cc_final: 0.5084 (ttt) REVERT: B 668 LYS cc_start: 0.8582 (mttm) cc_final: 0.8308 (mtmt) REVERT: C 89 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: C 95 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7326 (p90) REVERT: E 20 MET cc_start: 0.8209 (mtm) cc_final: 0.7958 (mtm) REVERT: E 180 GLN cc_start: 0.7544 (pm20) cc_final: 0.7304 (pm20) REVERT: E 185 THR cc_start: 0.8387 (p) cc_final: 0.8096 (p) REVERT: F 170 ASP cc_start: 0.8307 (t0) cc_final: 0.7809 (t0) outliers start: 41 outliers final: 30 residues processed: 216 average time/residue: 0.2767 time to fit residues: 90.3781 Evaluate side-chains 217 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 143 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN F 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16171 Z= 0.209 Angle : 0.567 10.712 21959 Z= 0.293 Chirality : 0.042 0.181 2503 Planarity : 0.004 0.044 2763 Dihedral : 4.432 40.383 2192 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 2.72 % Allowed : 13.39 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.06 (0.19), residues: 1994 helix: 1.74 (0.19), residues: 738 sheet: 1.03 (0.24), residues: 489 loop : -0.50 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 160 HIS 0.004 0.001 HIS B 150 PHE 0.015 0.001 PHE A 403 TYR 0.020 0.002 TYR B 571 ARG 0.006 0.000 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 189 time to evaluate : 2.021 Fit side-chains revert: symmetry clash REVERT: A 452 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7801 (mt-10) REVERT: A 480 MET cc_start: 0.7931 (mmm) cc_final: 0.7361 (mmt) REVERT: B 668 LYS cc_start: 0.8601 (mttm) cc_final: 0.8325 (mtmt) REVERT: C 89 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: C 95 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7349 (p90) REVERT: D 79 MET cc_start: 0.6935 (ttm) cc_final: 0.6494 (mtt) REVERT: E 20 MET cc_start: 0.8217 (mtm) cc_final: 0.7970 (mtm) REVERT: E 180 GLN cc_start: 0.7565 (pm20) cc_final: 0.7297 (pm20) REVERT: E 185 THR cc_start: 0.8390 (p) cc_final: 0.8100 (p) REVERT: F 170 ASP cc_start: 0.8277 (t0) cc_final: 0.7774 (t0) REVERT: F 189 HIS cc_start: 0.6486 (m-70) cc_final: 0.6237 (m90) outliers start: 48 outliers final: 39 residues processed: 222 average time/residue: 0.2703 time to fit residues: 91.3679 Evaluate side-chains 228 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 187 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 121 optimal weight: 0.1980 chunk 130 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 150 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16171 Z= 0.168 Angle : 0.550 9.457 21959 Z= 0.284 Chirality : 0.041 0.180 2503 Planarity : 0.004 0.043 2763 Dihedral : 4.344 39.881 2192 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 2.55 % Allowed : 13.67 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.17 (0.19), residues: 1994 helix: 1.87 (0.19), residues: 738 sheet: 1.07 (0.24), residues: 490 loop : -0.48 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 160 HIS 0.003 0.001 HIS A 510 PHE 0.028 0.001 PHE C 152 TYR 0.020 0.001 TYR B 571 ARG 0.006 0.000 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 193 time to evaluate : 1.866 Fit side-chains revert: symmetry clash REVERT: A 353 MET cc_start: 0.4839 (mmm) cc_final: 0.4607 (mmt) REVERT: A 452 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7767 (mt-10) REVERT: A 480 MET cc_start: 0.7919 (mmm) cc_final: 0.7349 (mmt) REVERT: B 615 MET cc_start: 0.5635 (tmm) cc_final: 0.5006 (ttt) REVERT: B 668 LYS cc_start: 0.8598 (mttm) cc_final: 0.8325 (mtmt) REVERT: C 89 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: C 95 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7321 (p90) REVERT: E 20 MET cc_start: 0.8153 (mtm) cc_final: 0.7884 (mtm) REVERT: E 109 MET cc_start: 0.8254 (mpp) cc_final: 0.8045 (mmt) REVERT: E 180 GLN cc_start: 0.7504 (pm20) cc_final: 0.7237 (pm20) REVERT: E 185 THR cc_start: 0.8401 (p) cc_final: 0.8086 (p) REVERT: F 170 ASP cc_start: 0.8260 (t0) cc_final: 0.7757 (t0) outliers start: 45 outliers final: 38 residues processed: 221 average time/residue: 0.2916 time to fit residues: 98.7345 Evaluate side-chains 225 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 185 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 0.0770 chunk 167 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 107 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN D 125 GLN F 89 GLN F 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16171 Z= 0.180 Angle : 0.557 8.766 21959 Z= 0.287 Chirality : 0.041 0.180 2503 Planarity : 0.004 0.043 2763 Dihedral : 4.308 40.065 2192 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 2.67 % Allowed : 13.90 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.20 (0.19), residues: 1994 helix: 1.89 (0.19), residues: 738 sheet: 1.08 (0.24), residues: 490 loop : -0.46 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 160 HIS 0.003 0.001 HIS B 150 PHE 0.014 0.001 PHE B 493 TYR 0.022 0.001 TYR E 131 ARG 0.005 0.000 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 192 time to evaluate : 1.808 Fit side-chains revert: symmetry clash REVERT: A 452 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7765 (mt-10) REVERT: A 480 MET cc_start: 0.7921 (mmm) cc_final: 0.7349 (mmt) REVERT: B 615 MET cc_start: 0.5617 (tmm) cc_final: 0.5113 (ttt) REVERT: B 668 LYS cc_start: 0.8602 (mttm) cc_final: 0.8329 (mtmt) REVERT: C 89 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: C 95 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7276 (p90) REVERT: D 79 MET cc_start: 0.6766 (ttm) cc_final: 0.6482 (mtp) REVERT: E 20 MET cc_start: 0.8160 (mtm) cc_final: 0.7894 (mtm) REVERT: E 180 GLN cc_start: 0.7506 (pm20) cc_final: 0.7231 (pm20) REVERT: E 185 THR cc_start: 0.8435 (p) cc_final: 0.8132 (p) REVERT: F 170 ASP cc_start: 0.8284 (t0) cc_final: 0.7753 (t0) REVERT: F 189 HIS cc_start: 0.6479 (m-70) cc_final: 0.6220 (m90) outliers start: 47 outliers final: 44 residues processed: 224 average time/residue: 0.2587 time to fit residues: 88.3201 Evaluate side-chains 235 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 189 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 182 optimal weight: 0.0870 chunk 157 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 168 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16171 Z= 0.163 Angle : 0.552 12.509 21959 Z= 0.283 Chirality : 0.041 0.210 2503 Planarity : 0.004 0.044 2763 Dihedral : 4.266 39.728 2192 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.76 % Favored : 96.14 % Rotamer: Outliers : 2.50 % Allowed : 14.01 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.28 (0.19), residues: 1994 helix: 1.98 (0.19), residues: 738 sheet: 1.12 (0.24), residues: 487 loop : -0.44 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.003 0.001 HIS F 189 PHE 0.013 0.001 PHE A 402 TYR 0.026 0.001 TYR C 108 ARG 0.008 0.000 ARG F 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 191 time to evaluate : 1.914 Fit side-chains revert: symmetry clash REVERT: A 353 MET cc_start: 0.4860 (mmm) cc_final: 0.4638 (mmt) REVERT: A 413 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7175 (tppt) REVERT: A 452 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7714 (mt-10) REVERT: A 480 MET cc_start: 0.7916 (mmm) cc_final: 0.7343 (mmt) REVERT: B 615 MET cc_start: 0.5546 (tmm) cc_final: 0.4968 (ttt) REVERT: B 668 LYS cc_start: 0.8601 (mttm) cc_final: 0.8328 (mtmt) REVERT: C 89 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: E 20 MET cc_start: 0.8165 (mtm) cc_final: 0.7898 (mtm) REVERT: E 180 GLN cc_start: 0.7501 (pm20) cc_final: 0.7231 (pm20) REVERT: E 185 THR cc_start: 0.8437 (p) cc_final: 0.8133 (p) REVERT: F 170 ASP cc_start: 0.8286 (t0) cc_final: 0.7746 (t0) outliers start: 44 outliers final: 41 residues processed: 221 average time/residue: 0.2703 time to fit residues: 90.5426 Evaluate side-chains 226 residues out of total 1763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 184 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 175 MET Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 203 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 66 optimal weight: 0.0270 chunk 162 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.156690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.124040 restraints weight = 21333.050| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.09 r_work: 0.3319 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16171 Z= 0.171 Angle : 0.558 12.238 21959 Z= 0.285 Chirality : 0.041 0.211 2503 Planarity : 0.004 0.043 2763 Dihedral : 4.246 40.082 2192 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.34 % Rotamer: Outliers : 2.72 % Allowed : 14.29 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.29 (0.19), residues: 1994 helix: 1.99 (0.19), residues: 739 sheet: 1.12 (0.24), residues: 487 loop : -0.43 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 109 HIS 0.002 0.001 HIS B 150 PHE 0.013 0.001 PHE B 493 TYR 0.020 0.001 TYR B 571 ARG 0.008 0.000 ARG F 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3656.52 seconds wall clock time: 67 minutes 16.33 seconds (4036.33 seconds total)