Starting phenix.real_space_refine on Sun Mar 24 15:53:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqz_27666/03_2024/8dqz_27666_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqz_27666/03_2024/8dqz_27666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqz_27666/03_2024/8dqz_27666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqz_27666/03_2024/8dqz_27666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqz_27666/03_2024/8dqz_27666_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dqz_27666/03_2024/8dqz_27666_trim.pdb" } resolution = 2.92 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= 0.043 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: 7 Type Number sf(0) Gaussians P 54 5.49 5 Mg 4 5.21 5 S 101 5.16 5 C 13421 2.51 5 N 3652 2.21 5 O 4220 1.98 5 H 21302 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A ASP 560": "OD1" <-> "OD2" Residue "A ASP 566": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A ASP 733": "OD1" <-> "OD2" Residue "A ASP 734": "OD1" <-> "OD2" Residue "A TYR 784": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B ASP 255": "OD1" <-> "OD2" Residue "C TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C ASP 243": "OD1" <-> "OD2" Residue "C ASP 255": "OD1" <-> "OD2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D ASP 199": "OD1" <-> "OD2" Residue "D ASP 227": "OD1" <-> "OD2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 195": "OD1" <-> "OD2" Residue "E GLU 214": "OE1" <-> "OE2" Residue "E GLU 245": "OE1" <-> "OE2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "E GLU 311": "OE1" <-> "OE2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "E GLU 343": "OE1" <-> "OE2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F ASP 93": "OD1" <-> "OD2" Residue "F TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 134": "OD1" <-> "OD2" Residue "F ASP 150": "OD1" <-> "OD2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "F ASP 240": "OD1" <-> "OD2" Residue "F PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 93": "OD1" <-> "OD2" Residue "G GLU 104": "OE1" <-> "OE2" Residue "G TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "G PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H ASP 41": "OD1" <-> "OD2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H ASP 105": "OD1" <-> "OD2" Residue "H ASP 187": "OD1" <-> "OD2" Residue "H ASP 214": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 42754 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 7832 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5084 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain: "C" Number of atoms: 5247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 5247 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain: "D" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5347 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 323} Chain: "E" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5698 Classifications: {'peptide': 354} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 339} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4055 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 4047 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "H" Number of atoms: 4023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 4023 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "I" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 706 Classifications: {'DNA': 22} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 21} Chain: "J" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 559 Classifications: {'DNA': 18} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.50, per 1000 atoms: 0.46 Number of scatterers: 42754 At special positions: 0 Unit cell: (124.726, 119.77, 144.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 101 16.00 P 54 15.00 Mg 4 11.99 O 4220 8.00 N 3652 7.00 C 13421 6.00 H 21302 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 33.65 Conformation dependent library (CDL) restraints added in 4.1 seconds 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4942 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 17 sheets defined 54.0% alpha, 15.0% beta 12 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 18.76 Creating SS restraints... Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 358 through 371 removed outlier: 3.565A pdb=" N GLY A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 400 through 407 removed outlier: 3.596A pdb=" N HIS A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 460 through 467 Proline residue: A 465 - end of helix Processing helix chain 'A' and resid 479 through 495 removed outlier: 3.629A pdb=" N ILE A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 513 through 525 Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 567 through 572 removed outlier: 4.017A pdb=" N ASN A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 4.316A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 609 through 632 Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.648A pdb=" N VAL A 656 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 690 Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'A' and resid 704 through 714 removed outlier: 4.142A pdb=" N THR A 708 " --> pdb=" O ASP A 704 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 720 Processing helix chain 'A' and resid 721 through 723 No H-bonds generated for 'chain 'A' and resid 721 through 723' Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.545A pdb=" N TYR A 735 " --> pdb=" O VAL A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 747 Processing helix chain 'A' and resid 750 through 754 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 763 through 777 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.640A pdb=" N ILE B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 3.885A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 129 through 134 removed outlier: 3.515A pdb=" N TYR B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.712A pdb=" N LYS B 149 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 150 " --> pdb=" O SER B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 150' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.617A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.535A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.510A pdb=" N LEU B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 321 Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.616A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.575A pdb=" N MET C 78 " --> pdb=" O ASN C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 74 through 78' Processing helix chain 'C' and resid 89 through 103 removed outlier: 4.023A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 122 Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.504A pdb=" N ARG C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.889A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 removed outlier: 4.081A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.854A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 312 removed outlier: 3.861A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 332 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 removed outlier: 3.789A pdb=" N VAL D 39 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 56 removed outlier: 4.607A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.858A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 142 through 145 Processing helix chain 'D' and resid 146 through 160 removed outlier: 4.622A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 209 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 291 Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 296 through 310 Processing helix chain 'D' and resid 315 through 334 removed outlier: 3.536A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.643A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.443A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.550A pdb=" N MET E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 103 No H-bonds generated for 'chain 'E' and resid 102 through 103' Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.614A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 4.314A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR E 161 " --> pdb=" O THR E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 225 Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 removed outlier: 3.846A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 334 removed outlier: 3.553A pdb=" N GLU E 330 " --> pdb=" O SER E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 354 removed outlier: 3.962A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 18 removed outlier: 3.993A pdb=" N PHE F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 55 No H-bonds generated for 'chain 'F' and resid 53 through 55' Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.989A pdb=" N GLN F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 222 removed outlier: 3.854A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 19 removed outlier: 4.394A pdb=" N PHE G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 81 Processing helix chain 'G' and resid 141 through 153 removed outlier: 4.027A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'H' and resid 9 through 19 removed outlier: 3.662A pdb=" N LYS H 13 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 80 removed outlier: 3.525A pdb=" N ARG H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 155 removed outlier: 3.802A pdb=" N GLN H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER H 155 " --> pdb=" O LEU H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 216 Processing helix chain 'H' and resid 217 through 221 removed outlier: 4.379A pdb=" N SER H 220 " --> pdb=" O LYS H 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 348 through 352 removed outlier: 6.216A pdb=" N ALA A 349 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS A 455 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 351 " --> pdb=" O CYS A 455 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASP A 373 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE A 422 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 375 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASP A 424 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLN A 377 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 497 through 498 removed outlier: 6.297A pdb=" N LYS A 497 " --> pdb=" O ILE A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 601 Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.346A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 82 removed outlier: 3.574A pdb=" N LEU C 146 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.550A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N CYS D 170 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE D 63 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 69 through 76 removed outlier: 6.014A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.338A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 57 through 62 removed outlier: 3.667A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU F 88 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE F 111 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 5.893A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE F 36 " --> pdb=" O GLN F 29 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 203 through 208 removed outlier: 5.677A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU G 88 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU G 59 " --> pdb=" O LYS G 5 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 66 through 71 removed outlier: 5.915A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU G 47 " --> pdb=" O PHE G 249 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 196 through 199 removed outlier: 3.550A pdb=" N LEU G 139 " --> pdb=" O VAL G 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 177 through 182 removed outlier: 4.215A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 47 through 52 removed outlier: 4.015A pdb=" N GLN H 38 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 87 through 91 Processing sheet with id=AB8, first strand: chain 'H' and resid 196 through 199 removed outlier: 6.271A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) 1104 hydrogen bonds defined for protein. 3129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 18.51 Time building geometry restraints manager: 34.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 21263 1.05 - 1.27: 3596 1.27 - 1.49: 8525 1.49 - 1.70: 9639 1.70 - 1.92: 159 Bond restraints: 43182 Sorted by residual: bond pdb=" C2' AGS D 402 " pdb=" C3' AGS D 402 " ideal model delta sigma weight residual 1.530 1.239 0.291 1.30e-02 5.92e+03 5.01e+02 bond pdb=" C2' AGS A 901 " pdb=" C3' AGS A 901 " ideal model delta sigma weight residual 1.530 1.239 0.291 1.30e-02 5.92e+03 5.00e+02 bond pdb=" C2' AGS C 402 " pdb=" C3' AGS C 402 " ideal model delta sigma weight residual 1.530 1.240 0.290 1.30e-02 5.92e+03 4.99e+02 bond pdb=" C2' AGS B 402 " pdb=" C3' AGS B 402 " ideal model delta sigma weight residual 1.530 1.240 0.290 1.30e-02 5.92e+03 4.98e+02 bond pdb=" C6 AGS B 402 " pdb=" N6 AGS B 402 " ideal model delta sigma weight residual 1.335 1.469 -0.134 1.00e-02 1.00e+04 1.79e+02 ... (remaining 43177 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.01: 935 107.01 - 113.75: 52812 113.75 - 120.49: 13562 120.49 - 127.23: 10804 127.23 - 133.97: 232 Bond angle restraints: 78345 Sorted by residual: angle pdb=" N1 AGS B 402 " pdb=" C2 AGS B 402 " pdb=" N3 AGS B 402 " ideal model delta sigma weight residual 128.80 120.05 8.75 8.41e-01 1.41e+00 1.08e+02 angle pdb=" N1 AGS D 402 " pdb=" C2 AGS D 402 " pdb=" N3 AGS D 402 " ideal model delta sigma weight residual 128.80 120.06 8.74 8.41e-01 1.41e+00 1.08e+02 angle pdb=" N1 AGS A 901 " pdb=" C2 AGS A 901 " pdb=" N3 AGS A 901 " ideal model delta sigma weight residual 128.80 120.07 8.73 8.41e-01 1.41e+00 1.08e+02 angle pdb=" N1 AGS C 402 " pdb=" C2 AGS C 402 " pdb=" N3 AGS C 402 " ideal model delta sigma weight residual 128.80 120.10 8.70 8.41e-01 1.41e+00 1.07e+02 angle pdb=" C5 AGS D 402 " pdb=" N7 AGS D 402 " pdb=" C8 AGS D 402 " ideal model delta sigma weight residual 103.67 107.97 -4.30 4.26e-01 5.51e+00 1.02e+02 ... (remaining 78340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.18: 19095 32.18 - 64.35: 801 64.35 - 96.53: 32 96.53 - 128.70: 2 128.70 - 160.88: 4 Dihedral angle restraints: 19934 sinusoidal: 11325 harmonic: 8609 Sorted by residual: dihedral pdb=" O2B GDP E 401 " pdb=" O3A GDP E 401 " pdb=" PB GDP E 401 " pdb=" PA GDP E 401 " ideal model delta sinusoidal sigma weight residual 180.00 19.12 160.88 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C5' GDP E 401 " pdb=" O5' GDP E 401 " pdb=" PA GDP E 401 " pdb=" O3A GDP E 401 " ideal model delta sinusoidal sigma weight residual 179.98 -72.73 -107.29 1 2.00e+01 2.50e-03 3.11e+01 dihedral pdb=" O1A AGS D 402 " pdb=" O3A AGS D 402 " pdb=" PA AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sinusoidal sigma weight residual -67.73 68.86 -136.59 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 19931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3062 0.061 - 0.122: 364 0.122 - 0.183: 29 0.183 - 0.244: 6 0.244 - 0.305: 4 Chirality restraints: 3465 Sorted by residual: chirality pdb=" C2' AGS B 402 " pdb=" C1' AGS B 402 " pdb=" C3' AGS B 402 " pdb=" O2' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.37 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C2' AGS D 402 " pdb=" C1' AGS D 402 " pdb=" C3' AGS D 402 " pdb=" O2' AGS D 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C2' AGS C 402 " pdb=" C1' AGS C 402 " pdb=" C3' AGS C 402 " pdb=" O2' AGS C 402 " both_signs ideal model delta sigma weight residual False -2.67 -2.38 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 3462 not shown) Planarity restraints: 6173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 245 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" CD GLU E 245 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU E 245 " -0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU E 245 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 245 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C GLU E 245 " 0.042 2.00e-02 2.50e+03 pdb=" O GLU E 245 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU E 246 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 253 " 0.155 9.50e-02 1.11e+02 5.19e-02 2.95e+00 pdb=" NE ARG B 253 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 253 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 253 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 253 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG B 253 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 253 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 253 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 253 " 0.001 2.00e-02 2.50e+03 ... (remaining 6170 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1483 2.16 - 2.77: 83609 2.77 - 3.38: 120379 3.38 - 3.99: 157873 3.99 - 4.60: 244963 Nonbonded interactions: 608307 Sorted by model distance: nonbonded pdb=" OD1 ASP D 247 " pdb=" H LYS D 249 " model vdw 1.551 1.850 nonbonded pdb=" O LYS G 31 " pdb=" HH TYR G 60 " model vdw 1.553 1.850 nonbonded pdb=" OD1 ASP H 187 " pdb=" H HIS H 190 " model vdw 1.571 1.850 nonbonded pdb=" OE1 GLU F 32 " pdb=" H GLU F 32 " model vdw 1.574 1.850 nonbonded pdb=" OE1 GLU F 189 " pdb=" H GLU F 189 " model vdw 1.587 1.850 ... (remaining 608302 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'F' and resid 0 through 254) selection = (chain 'G' and ((resid 0 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 1 through 254)) selection = (chain 'H' and ((resid 0 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 1 through 254)) } 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: 2.670 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: 0.640 Extract box with map and model: 13.910 Check model and map are aligned: 0.700 Set scattering table: 0.430 Process input model: 151.820 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 185.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.291 21880 Z= 0.495 Angle : 0.598 11.174 29759 Z= 0.402 Chirality : 0.041 0.305 3465 Planarity : 0.003 0.068 3639 Dihedral : 16.920 160.881 8366 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.30 % Allowed : 16.41 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.18), residues: 2581 helix: 1.95 (0.16), residues: 1192 sheet: 0.52 (0.23), residues: 521 loop : 0.08 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 638 HIS 0.002 0.000 HIS A 610 PHE 0.016 0.001 PHE G 239 TYR 0.019 0.001 TYR A 352 ARG 0.004 0.000 ARG F 149 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 340 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 333 time to evaluate : 3.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.8211 (mmm) cc_final: 0.7878 (mmm) REVERT: G 188 MET cc_start: 0.6809 (tpp) cc_final: 0.6488 (tpp) REVERT: G 199 MET cc_start: 0.7240 (tmm) cc_final: 0.6959 (tmm) REVERT: H 1 MET cc_start: 0.1145 (tmt) cc_final: -0.0229 (mtm) REVERT: H 70 MET cc_start: 0.0402 (ttm) cc_final: -0.0809 (mtt) REVERT: H 133 TYR cc_start: 0.0961 (m-80) cc_final: 0.0542 (m-80) REVERT: H 150 ASP cc_start: 0.6797 (m-30) cc_final: 0.6021 (m-30) REVERT: H 174 ASP cc_start: 0.7603 (p0) cc_final: 0.6930 (t0) REVERT: H 199 MET cc_start: 0.4399 (ptm) cc_final: 0.3905 (ptp) outliers start: 7 outliers final: 4 residues processed: 340 average time/residue: 3.3522 time to fit residues: 1276.1018 Evaluate side-chains 178 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 3.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain F residue 78 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 234 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN A 377 GLN ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN A 636 GLN B 320 ASN C 202 ASN D 207 GLN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 153 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21880 Z= 0.274 Angle : 0.557 7.161 29759 Z= 0.292 Chirality : 0.040 0.167 3465 Planarity : 0.004 0.069 3639 Dihedral : 13.351 164.808 3275 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.30 % Allowed : 18.71 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.17), residues: 2581 helix: 1.69 (0.16), residues: 1216 sheet: 0.61 (0.24), residues: 516 loop : -0.15 (0.23), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 742 HIS 0.006 0.001 HIS B 232 PHE 0.015 0.001 PHE H 237 TYR 0.011 0.001 TYR D 286 ARG 0.011 0.001 ARG C 240 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 174 time to evaluate : 3.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.8281 (mmm) cc_final: 0.7940 (mmm) REVERT: G 36 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8817 (pp) REVERT: H 1 MET cc_start: 0.1120 (OUTLIER) cc_final: -0.0230 (mtm) REVERT: H 139 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7344 (pt) REVERT: H 150 ASP cc_start: 0.6918 (m-30) cc_final: 0.6230 (m-30) REVERT: H 174 ASP cc_start: 0.7538 (p0) cc_final: 0.6865 (t0) REVERT: H 188 MET cc_start: 0.7386 (mmm) cc_final: 0.7154 (mmm) outliers start: 53 outliers final: 21 residues processed: 219 average time/residue: 2.8875 time to fit residues: 725.2978 Evaluate side-chains 179 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 220 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 chunk 253 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 232 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 21880 Z= 0.350 Angle : 0.561 6.220 29759 Z= 0.299 Chirality : 0.041 0.168 3465 Planarity : 0.004 0.059 3639 Dihedral : 13.508 176.907 3271 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.52 % Allowed : 17.75 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2581 helix: 1.51 (0.15), residues: 1209 sheet: 0.51 (0.23), residues: 524 loop : -0.34 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 742 HIS 0.009 0.001 HIS B 232 PHE 0.013 0.001 PHE E 328 TYR 0.021 0.001 TYR G 211 ARG 0.009 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 166 time to evaluate : 3.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.8262 (mmm) cc_final: 0.7963 (mmm) REVERT: A 745 ILE cc_start: 0.9118 (mt) cc_final: 0.8881 (mt) REVERT: D 55 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8614 (t) REVERT: H 1 MET cc_start: 0.1301 (OUTLIER) cc_final: -0.0209 (mtm) REVERT: H 150 ASP cc_start: 0.6858 (m-30) cc_final: 0.6247 (m-30) REVERT: H 174 ASP cc_start: 0.7479 (p0) cc_final: 0.6811 (t0) REVERT: H 188 MET cc_start: 0.7429 (mmm) cc_final: 0.7202 (mmm) outliers start: 58 outliers final: 28 residues processed: 217 average time/residue: 2.5959 time to fit residues: 653.0590 Evaluate side-chains 186 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 220 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 0.0570 chunk 176 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 235 optimal weight: 10.0000 chunk 249 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 223 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21880 Z= 0.192 Angle : 0.509 6.131 29759 Z= 0.268 Chirality : 0.039 0.180 3465 Planarity : 0.004 0.070 3639 Dihedral : 13.367 167.908 3271 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.39 % Allowed : 18.75 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.17), residues: 2581 helix: 1.70 (0.16), residues: 1211 sheet: 0.47 (0.23), residues: 526 loop : -0.23 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 742 HIS 0.004 0.001 HIS B 232 PHE 0.009 0.001 PHE E 328 TYR 0.016 0.001 TYR G 211 ARG 0.010 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.8237 (mmm) cc_final: 0.7886 (mmm) REVERT: A 745 ILE cc_start: 0.9085 (mt) cc_final: 0.8834 (mt) REVERT: H 1 MET cc_start: 0.1276 (OUTLIER) cc_final: -0.0217 (mtm) REVERT: H 149 ARG cc_start: 0.7590 (ptm160) cc_final: 0.7345 (ppt-90) REVERT: H 174 ASP cc_start: 0.7528 (p0) cc_final: 0.6888 (t70) REVERT: H 188 MET cc_start: 0.7453 (mmm) cc_final: 0.7219 (mmm) REVERT: H 217 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6775 (mtpt) outliers start: 32 outliers final: 15 residues processed: 189 average time/residue: 2.7563 time to fit residues: 600.1796 Evaluate side-chains 166 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 217 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 212 optimal weight: 0.5980 chunk 172 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21880 Z= 0.235 Angle : 0.506 5.990 29759 Z= 0.268 Chirality : 0.039 0.170 3465 Planarity : 0.004 0.075 3639 Dihedral : 13.333 168.713 3271 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.52 % Allowed : 18.36 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.17), residues: 2581 helix: 1.72 (0.16), residues: 1210 sheet: 0.46 (0.23), residues: 528 loop : -0.23 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 742 HIS 0.005 0.001 HIS B 232 PHE 0.009 0.001 PHE E 328 TYR 0.015 0.001 TYR E 135 ARG 0.010 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 155 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.8260 (mmm) cc_final: 0.7897 (mmm) REVERT: A 350 MET cc_start: 0.8943 (tmm) cc_final: 0.8712 (tpp) REVERT: A 398 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.7954 (t0) REVERT: A 745 ILE cc_start: 0.9119 (mt) cc_final: 0.8884 (mt) REVERT: G 1 MET cc_start: 0.8206 (ttm) cc_final: 0.7644 (ttm) REVERT: H 1 MET cc_start: 0.1275 (OUTLIER) cc_final: -0.0183 (mtm) REVERT: H 149 ARG cc_start: 0.7652 (ptm160) cc_final: 0.7284 (ppt-90) REVERT: H 174 ASP cc_start: 0.7532 (p0) cc_final: 0.6872 (t70) REVERT: H 188 MET cc_start: 0.7433 (mmm) cc_final: 0.7185 (mmm) outliers start: 35 outliers final: 19 residues processed: 187 average time/residue: 2.8439 time to fit residues: 617.2985 Evaluate side-chains 168 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 3.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 131 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 249 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21880 Z= 0.164 Angle : 0.490 5.879 29759 Z= 0.258 Chirality : 0.038 0.175 3465 Planarity : 0.003 0.080 3639 Dihedral : 13.263 166.927 3271 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.22 % Allowed : 18.75 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.17), residues: 2581 helix: 1.80 (0.16), residues: 1218 sheet: 0.48 (0.23), residues: 528 loop : -0.16 (0.23), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 742 HIS 0.003 0.001 HIS B 232 PHE 0.016 0.001 PHE G 248 TYR 0.016 0.001 TYR H 133 ARG 0.011 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 4.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.8277 (mmm) cc_final: 0.7915 (mmm) REVERT: A 745 ILE cc_start: 0.9123 (mt) cc_final: 0.8888 (mt) REVERT: G 1 MET cc_start: 0.8196 (ttm) cc_final: 0.7737 (ttm) REVERT: H 1 MET cc_start: 0.1055 (tmt) cc_final: -0.0249 (mtm) REVERT: H 149 ARG cc_start: 0.7578 (ptm160) cc_final: 0.7241 (ppt-90) REVERT: H 174 ASP cc_start: 0.7541 (p0) cc_final: 0.6904 (t0) REVERT: H 188 MET cc_start: 0.7438 (mmm) cc_final: 0.7165 (mmm) outliers start: 28 outliers final: 16 residues processed: 175 average time/residue: 2.9196 time to fit residues: 586.3275 Evaluate side-chains 158 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 3.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 162 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 210 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN H 153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21880 Z= 0.283 Angle : 0.520 6.334 29759 Z= 0.276 Chirality : 0.040 0.165 3465 Planarity : 0.004 0.085 3639 Dihedral : 13.322 170.167 3271 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.22 % Allowed : 18.58 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.17), residues: 2581 helix: 1.76 (0.15), residues: 1212 sheet: 0.55 (0.23), residues: 520 loop : -0.22 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 742 HIS 0.007 0.001 HIS B 232 PHE 0.016 0.001 PHE F 125 TYR 0.021 0.001 TYR G 211 ARG 0.012 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 3.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.8320 (mmm) cc_final: 0.7968 (mmm) REVERT: A 398 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.7990 (t0) REVERT: A 745 ILE cc_start: 0.9168 (mt) cc_final: 0.8954 (mt) REVERT: G 1 MET cc_start: 0.8273 (ttm) cc_final: 0.8066 (ttm) REVERT: H 149 ARG cc_start: 0.7608 (ptm160) cc_final: 0.7270 (ppt-90) REVERT: H 174 ASP cc_start: 0.7547 (p0) cc_final: 0.6876 (t0) outliers start: 28 outliers final: 18 residues processed: 174 average time/residue: 2.8443 time to fit residues: 568.9690 Evaluate side-chains 164 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain H residue 131 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21880 Z= 0.254 Angle : 0.513 9.659 29759 Z= 0.271 Chirality : 0.039 0.182 3465 Planarity : 0.004 0.091 3639 Dihedral : 13.335 169.583 3271 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.35 % Allowed : 18.88 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.17), residues: 2581 helix: 1.77 (0.15), residues: 1213 sheet: 0.43 (0.23), residues: 526 loop : -0.17 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 742 HIS 0.006 0.001 HIS B 232 PHE 0.014 0.001 PHE H 237 TYR 0.017 0.001 TYR H 133 ARG 0.012 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 149 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.7960 (t0) REVERT: A 745 ILE cc_start: 0.9177 (mt) cc_final: 0.8972 (mt) REVERT: G 1 MET cc_start: 0.8297 (ttm) cc_final: 0.8091 (ttm) REVERT: H 1 MET cc_start: 0.1219 (tmt) cc_final: 0.0087 (mtm) REVERT: H 149 ARG cc_start: 0.7581 (ptm160) cc_final: 0.7249 (ppt-90) REVERT: H 174 ASP cc_start: 0.7548 (p0) cc_final: 0.6889 (t0) outliers start: 31 outliers final: 17 residues processed: 176 average time/residue: 3.0235 time to fit residues: 606.0309 Evaluate side-chains 164 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 36 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 30.0000 chunk 217 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21880 Z= 0.248 Angle : 0.514 9.916 29759 Z= 0.271 Chirality : 0.039 0.214 3465 Planarity : 0.004 0.095 3639 Dihedral : 13.330 170.139 3271 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.91 % Allowed : 19.31 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.17), residues: 2581 helix: 1.79 (0.15), residues: 1213 sheet: 0.43 (0.23), residues: 528 loop : -0.14 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 742 HIS 0.006 0.001 HIS B 232 PHE 0.016 0.001 PHE H 237 TYR 0.018 0.001 TYR E 135 ARG 0.015 0.000 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 4.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.8980 (tmm) cc_final: 0.8711 (tpp) REVERT: A 398 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.7956 (t0) REVERT: A 745 ILE cc_start: 0.9187 (mt) cc_final: 0.8984 (mt) REVERT: H 1 MET cc_start: 0.1297 (tmt) cc_final: 0.0141 (mtm) REVERT: H 149 ARG cc_start: 0.7590 (ptm160) cc_final: 0.7251 (ppt-90) REVERT: H 174 ASP cc_start: 0.7548 (p0) cc_final: 0.6885 (t0) outliers start: 21 outliers final: 16 residues processed: 170 average time/residue: 3.0247 time to fit residues: 589.0951 Evaluate side-chains 159 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 3.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain G residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 257 optimal weight: 10.0000 chunk 236 optimal weight: 20.0000 chunk 204 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21880 Z= 0.215 Angle : 0.515 10.457 29759 Z= 0.270 Chirality : 0.039 0.231 3465 Planarity : 0.004 0.098 3639 Dihedral : 13.150 169.346 3268 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.04 % Allowed : 19.49 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2581 helix: 1.85 (0.16), residues: 1214 sheet: 0.47 (0.23), residues: 530 loop : -0.15 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 259 HIS 0.004 0.001 HIS B 232 PHE 0.018 0.001 PHE H 237 TYR 0.036 0.001 TYR G 133 ARG 0.015 0.000 ARG E 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue SER 0 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.8987 (tmm) cc_final: 0.8700 (tpp) REVERT: A 398 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.7945 (t0) REVERT: G 1 MET cc_start: 0.8126 (ttm) cc_final: 0.7667 (ttm) REVERT: H 1 MET cc_start: 0.1163 (tmt) cc_final: 0.0063 (mtm) REVERT: H 149 ARG cc_start: 0.7573 (ptm160) cc_final: 0.7230 (ppt-90) REVERT: H 174 ASP cc_start: 0.7540 (p0) cc_final: 0.6868 (t0) outliers start: 24 outliers final: 18 residues processed: 166 average time/residue: 2.9850 time to fit residues: 571.8442 Evaluate side-chains 160 residues out of total 2308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 133 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.110399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.069117 restraints weight = 113498.432| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.81 r_work: 0.2836 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21880 Z= 0.211 Angle : 0.508 10.689 29759 Z= 0.266 Chirality : 0.039 0.193 3465 Planarity : 0.004 0.098 3639 Dihedral : 13.127 169.439 3268 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.91 % Allowed : 19.40 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2581 helix: 1.87 (0.16), residues: 1215 sheet: 0.40 (0.23), residues: 536 loop : -0.13 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 742 HIS 0.005 0.001 HIS B 232 PHE 0.017 0.001 PHE H 237 TYR 0.021 0.001 TYR G 211 ARG 0.014 0.000 ARG E 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13059.05 seconds wall clock time: 228 minutes 55.76 seconds (13735.76 seconds total)