Starting phenix.real_space_refine on Sun Mar 17 18:08:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb2_31049/03_2024/7eb2_31049_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb2_31049/03_2024/7eb2_31049.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb2_31049/03_2024/7eb2_31049_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb2_31049/03_2024/7eb2_31049_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb2_31049/03_2024/7eb2_31049_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb2_31049/03_2024/7eb2_31049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb2_31049/03_2024/7eb2_31049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb2_31049/03_2024/7eb2_31049_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb2_31049/03_2024/7eb2_31049_updated.pdb" } resolution = 3.5 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= 0.002 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 114 5.16 5 Cl 1 4.86 5 C 11829 2.51 5 N 3116 2.21 5 O 3434 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 32": "NH1" <-> "NH2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 246": "OE1" <-> "OE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "C PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 497": "OD1" <-> "OD2" Residue "C PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 558": "OD1" <-> "OD2" Residue "C PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 721": "OD1" <-> "OD2" Residue "C PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 801": "OD1" <-> "OD2" Residue "C PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 228": "OD1" <-> "OD2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 235": "OD1" <-> "OD2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 286": "OE1" <-> "OE2" Residue "D GLU 341": "OE1" <-> "OE2" Residue "D PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 374": "OE1" <-> "OE2" Residue "D TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 392": "OD1" <-> "OD2" Residue "D PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 433": "OD1" <-> "OD2" Residue "D GLU 436": "OE1" <-> "OE2" Residue "D GLU 441": "OE1" <-> "OE2" Residue "D ASP 447": "OD1" <-> "OD2" Residue "D PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 550": "OE1" <-> "OE2" Residue "D ASP 594": "OD1" <-> "OD2" Residue "D ARG 622": "NH1" <-> "NH2" Residue "D TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 715": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18497 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2820 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 347} Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "Y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "C" Number of atoms: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5406 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 28, 'TRANS': 649} Chain breaks: 2 Chain: "D" Number of atoms: 5414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5414 Classifications: {'peptide': 680} Link IDs: {'PTRANS': 26, 'TRANS': 653} Chain breaks: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'2C0': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'FN0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.15, per 1000 atoms: 0.55 Number of scatterers: 18497 At special positions: 0 Unit cell: (142.974, 121.68, 226.122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 114 16.00 F 3 9.00 O 3434 8.00 N 3116 7.00 C 11829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 159 " - pdb=" SG CYS N 229 " distance=2.20 Simple disulfide: pdb=" SG CYS C 220 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 135 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 648 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.91 Conformation dependent library (CDL) restraints added in 3.6 seconds 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 21 sheets defined 40.4% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.573A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 removed outlier: 3.849A pdb=" N ILE A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 89 removed outlier: 3.628A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 removed outlier: 3.717A pdb=" N ASP A 103 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 113 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.794A pdb=" N PHE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 162 removed outlier: 4.369A pdb=" N ALA A 153 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 156 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASP A 158 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASP A 160 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 162 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 178 removed outlier: 4.597A pdb=" N ARG A 176 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.862A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 4.023A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.697A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'Y' and resid 7 through 22 Processing helix chain 'Y' and resid 30 through 43 Processing helix chain 'Y' and resid 45 through 47 No H-bonds generated for 'chain 'Y' and resid 45 through 47' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'N' and resid 221 through 223 No H-bonds generated for 'chain 'N' and resid 221 through 223' Processing helix chain 'C' and resid 185 through 201 Proline residue: C 190 - end of helix Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 272 through 275 Processing helix chain 'C' and resid 290 through 304 removed outlier: 3.681A pdb=" N HIS C 293 " --> pdb=" O ALA C 290 " (cutoff:3.500A) Proline residue: C 295 - end of helix removed outlier: 3.747A pdb=" N LYS C 303 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP C 304 " --> pdb=" O PHE C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 330 Processing helix chain 'C' and resid 348 through 356 Processing helix chain 'C' and resid 368 through 381 removed outlier: 4.450A pdb=" N LYS C 373 " --> pdb=" O THR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 418 removed outlier: 3.694A pdb=" N GLU C 417 " --> pdb=" O ASP C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 453 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 464 through 484 removed outlier: 3.573A pdb=" N ALA C 467 " --> pdb=" O PHE C 464 " (cutoff:3.500A) Proline residue: C 468 - end of helix Processing helix chain 'C' and resid 504 through 514 Processing helix chain 'C' and resid 589 through 615 Processing helix chain 'C' and resid 621 through 623 No H-bonds generated for 'chain 'C' and resid 621 through 623' Processing helix chain 'C' and resid 627 through 648 removed outlier: 4.157A pdb=" N VAL C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE C 645 " --> pdb=" O LEU C 641 " (cutoff:3.500A) Proline residue: C 646 - end of helix Processing helix chain 'C' and resid 659 through 692 removed outlier: 4.160A pdb=" N SER C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N MET C 681 " --> pdb=" O GLY C 677 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE C 692 " --> pdb=" O VAL C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 731 removed outlier: 3.787A pdb=" N TYR C 711 " --> pdb=" O PRO C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 769 through 790 Processing helix chain 'C' and resid 802 through 828 Proline residue: C 821 - end of helix removed outlier: 3.703A pdb=" N MET C 824 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER C 828 " --> pdb=" O MET C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 859 Proline residue: C 855 - end of helix Processing helix chain 'D' and resid 69 through 91 removed outlier: 3.836A pdb=" N LEU D 78 " --> pdb=" O ARG D 75 " (cutoff:3.500A) Proline residue: D 79 - end of helix removed outlier: 3.742A pdb=" N GLU D 91 " --> pdb=" O ILE D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 136 through 149 removed outlier: 3.617A pdb=" N SER D 145 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLN D 147 " --> pdb=" O ALA D 143 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLY D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TRP D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 164 Processing helix chain 'D' and resid 183 through 193 Processing helix chain 'D' and resid 206 through 218 removed outlier: 4.055A pdb=" N GLY D 217 " --> pdb=" O ASN D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 246 removed outlier: 3.554A pdb=" N VAL D 240 " --> pdb=" O CYS D 237 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS D 241 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY D 245 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 269 removed outlier: 3.844A pdb=" N ALA D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS D 262 " --> pdb=" O ASN D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 310 Processing helix chain 'D' and resid 335 through 345 Processing helix chain 'D' and resid 355 through 374 Processing helix chain 'D' and resid 393 through 405 removed outlier: 3.864A pdb=" N GLU D 405 " --> pdb=" O ASN D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 504 Processing helix chain 'D' and resid 510 through 514 Processing helix chain 'D' and resid 517 through 533 Processing helix chain 'D' and resid 535 through 538 No H-bonds generated for 'chain 'D' and resid 535 through 538' Processing helix chain 'D' and resid 548 through 583 removed outlier: 3.988A pdb=" N THR D 554 " --> pdb=" O GLU D 550 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR D 557 " --> pdb=" O CYS D 553 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 618 Processing helix chain 'D' and resid 653 through 677 Processing helix chain 'D' and resid 689 through 713 removed outlier: 3.908A pdb=" N PHE D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 746 removed outlier: 4.418A pdb=" N VAL D 739 " --> pdb=" O THR D 735 " (cutoff:3.500A) Proline residue: D 742 - end of helix removed outlier: 3.891A pdb=" N THR D 746 " --> pdb=" O PRO D 742 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.738A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.743A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.916A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 149 through 153 removed outlier: 6.885A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.869A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.537A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.387A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.772A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.643A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.094A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'N' and resid 226 through 231 removed outlier: 6.093A pdb=" N LEU N 178 " --> pdb=" O LEU N 187 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU N 187 " --> pdb=" O LEU N 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 168 through 175 Processing sheet with id= N, first strand: chain 'C' and resid 264 through 266 Processing sheet with id= O, first strand: chain 'C' and resid 547 through 554 removed outlier: 6.497A pdb=" N ILE C 539 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TYR C 552 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR C 537 " --> pdb=" O TYR C 552 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR C 425 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE C 393 " --> pdb=" O GLY C 364 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LYS C 308 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N VAL C 363 " --> pdb=" O LYS C 308 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 310 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU C 365 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE C 312 " --> pdb=" O LEU C 365 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU C 336 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N THR C 311 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N THR C 338 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 12.466A pdb=" N GLN C 313 " --> pdb=" O THR C 338 " (cutoff:3.500A) removed outlier: 9.802A pdb=" N ARG C 340 " --> pdb=" O GLN C 313 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 517 through 520 removed outlier: 3.511A pdb=" N PHE C 518 " --> pdb=" O VAL C 525 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 735 through 740 removed outlier: 3.515A pdb=" N THR C 737 " --> pdb=" O HIS C 760 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 99 through 105 removed outlier: 5.772A pdb=" N LEU D 56 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ARG D 102 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE D 58 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR D 104 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY D 60 " --> pdb=" O TYR D 104 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET D 129 " --> pdb=" O MET D 59 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU D 61 " --> pdb=" O MET D 129 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE D 131 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL D 152 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLY D 132 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU D 154 " --> pdb=" O GLY D 132 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 229 through 232 removed outlier: 8.411A pdb=" N GLU D 230 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR D 200 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N PHE D 232 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR D 202 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE D 250 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU D 201 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU D 252 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLN D 203 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLN D 254 " --> pdb=" O GLN D 203 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN D 278 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLY D 253 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE D 280 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE D 315 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 440 " --> pdb=" O PHE D 428 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLN D 430 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LYS D 438 " --> pdb=" O GLN D 430 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN D 432 " --> pdb=" O GLU D 436 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLU D 436 " --> pdb=" O GLN D 432 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 407 through 410 removed outlier: 3.597A pdb=" N PHE D 408 " --> pdb=" O VAL D 415 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 469 through 474 removed outlier: 3.565A pdb=" N TYR D 628 " --> pdb=" O PRO D 643 " (cutoff:3.500A) 818 hydrogen bonds defined for protein. 2196 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.45 Time building geometry restraints manager: 8.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3187 1.32 - 1.44: 5001 1.44 - 1.57: 10533 1.57 - 1.69: 0 1.69 - 1.82: 175 Bond restraints: 18896 Sorted by residual: bond pdb=" C6 FN0 D 901 " pdb=" O1 FN0 D 901 " ideal model delta sigma weight residual 1.514 1.374 0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" CA HIS D 579 " pdb=" C HIS D 579 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" C13 FN0 D 901 " pdb=" O1 FN0 D 901 " ideal model delta sigma weight residual 1.422 1.349 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C13 FN0 D 901 " pdb=" O3 FN0 D 901 " ideal model delta sigma weight residual 1.185 1.256 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C GLU A 65 " pdb=" O GLU A 65 " ideal model delta sigma weight residual 1.236 1.199 0.038 1.25e-02 6.40e+03 9.03e+00 ... (remaining 18891 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.26: 428 106.26 - 113.20: 10218 113.20 - 120.14: 7150 120.14 - 127.08: 7589 127.08 - 134.02: 215 Bond angle restraints: 25600 Sorted by residual: angle pdb=" N ALA A 31 " pdb=" CA ALA A 31 " pdb=" C ALA A 31 " ideal model delta sigma weight residual 111.28 121.92 -10.64 1.09e+00 8.42e-01 9.54e+01 angle pdb=" N ARG A 32 " pdb=" CA ARG A 32 " pdb=" C ARG A 32 " ideal model delta sigma weight residual 111.28 120.47 -9.19 1.09e+00 8.42e-01 7.11e+01 angle pdb=" N LYS D 586 " pdb=" CA LYS D 586 " pdb=" C LYS D 586 " ideal model delta sigma weight residual 111.33 101.47 9.86 1.21e+00 6.83e-01 6.64e+01 angle pdb=" N LYS A 70 " pdb=" CA LYS A 70 " pdb=" C LYS A 70 " ideal model delta sigma weight residual 111.28 102.96 8.32 1.09e+00 8.42e-01 5.83e+01 angle pdb=" N ASP D 594 " pdb=" CA ASP D 594 " pdb=" C ASP D 594 " ideal model delta sigma weight residual 111.36 119.67 -8.31 1.09e+00 8.42e-01 5.82e+01 ... (remaining 25595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 10577 17.85 - 35.70: 563 35.70 - 53.56: 86 53.56 - 71.41: 12 71.41 - 89.26: 19 Dihedral angle restraints: 11257 sinusoidal: 4472 harmonic: 6785 Sorted by residual: dihedral pdb=" CB CYS N 159 " pdb=" SG CYS N 159 " pdb=" SG CYS N 229 " pdb=" CB CYS N 229 " ideal model delta sinusoidal sigma weight residual 93.00 136.65 -43.65 1 1.00e+01 1.00e-02 2.65e+01 dihedral pdb=" CB CYS C 220 " pdb=" SG CYS C 220 " pdb=" SG CYS C 246 " pdb=" CB CYS C 246 " ideal model delta sinusoidal sigma weight residual 93.00 132.51 -39.51 1 1.00e+01 1.00e-02 2.19e+01 dihedral pdb=" CA GLN D 432 " pdb=" C GLN D 432 " pdb=" N ASP D 433 " pdb=" CA ASP D 433 " ideal model delta harmonic sigma weight residual -180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 11254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.094: 2873 1.094 - 2.187: 0 2.187 - 3.281: 0 3.281 - 4.374: 0 4.374 - 5.468: 1 Chirality restraints: 2874 Sorted by residual: chirality pdb=" C7 FN0 D 901 " pdb=" C13 FN0 D 901 " pdb=" C17 FN0 D 901 " pdb=" C5 FN0 D 901 " both_signs ideal model delta sigma weight residual False -2.69 2.78 -5.47 2.00e-01 2.50e+01 7.47e+02 chirality pdb=" CA ALA A 31 " pdb=" N ALA A 31 " pdb=" C ALA A 31 " pdb=" CB ALA A 31 " both_signs ideal model delta sigma weight residual False 2.48 2.13 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA ALA D 580 " pdb=" N ALA D 580 " pdb=" C ALA D 580 " pdb=" CB ALA D 580 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 2871 not shown) Planarity restraints: 3237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 FN0 D 901 " 0.094 2.00e-02 2.50e+03 5.44e-02 2.96e+01 pdb=" C7 FN0 D 901 " -0.028 2.00e-02 2.50e+03 pdb=" O1 FN0 D 901 " -0.029 2.00e-02 2.50e+03 pdb=" O3 FN0 D 901 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 214 " -0.016 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C CYS A 214 " 0.059 2.00e-02 2.50e+03 pdb=" O CYS A 214 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A 215 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 201 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C VAL A 201 " -0.058 2.00e-02 2.50e+03 pdb=" O VAL A 201 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY A 202 " 0.019 2.00e-02 2.50e+03 ... (remaining 3234 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 236 2.65 - 3.22: 17699 3.22 - 3.78: 27627 3.78 - 4.34: 39432 4.34 - 4.90: 64200 Nonbonded interactions: 149194 Sorted by model distance: nonbonded pdb=" O LEU A 353 " pdb=" C LYS D 513 " model vdw 2.092 3.270 nonbonded pdb=" N GLU A 63 " pdb=" OE1 GLU A 63 " model vdw 2.167 2.520 nonbonded pdb=" OG1 THR C 633 " pdb=" OG SER C 680 " model vdw 2.187 2.440 nonbonded pdb=" OE2 GLU N 6 " pdb=" N GLY N 114 " model vdw 2.190 2.520 nonbonded pdb=" O LYS A 210 " pdb=" ND1 HIS A 213 " model vdw 2.209 2.520 ... (remaining 149189 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.490 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: 0.000 Extract box with map and model: 7.490 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 52.330 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 : 0.007 0.140 18896 Z= 0.456 Angle : 0.763 11.268 25600 Z= 0.497 Chirality : 0.115 5.468 2874 Planarity : 0.004 0.054 3237 Dihedral : 11.772 89.258 6877 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.59 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % 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: -1.24 (0.16), residues: 2315 helix: -0.43 (0.15), residues: 947 sheet: -0.35 (0.24), residues: 453 loop : -1.35 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.005 0.001 HIS D 355 PHE 0.015 0.001 PHE C 375 TYR 0.013 0.001 TYR D 314 ARG 0.004 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 701 time to evaluate : 2.217 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: 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 10 LYS cc_start: 0.9095 (mttt) cc_final: 0.8640 (mtmm) REVERT: A 25 GLU cc_start: 0.8502 (tt0) cc_final: 0.8153 (pt0) REVERT: A 154 TYR cc_start: 0.8094 (m-80) cc_final: 0.7796 (m-80) REVERT: A 194 LEU cc_start: 0.8162 (mp) cc_final: 0.7715 (tp) REVERT: A 198 MET cc_start: 0.8336 (ttm) cc_final: 0.8070 (ttm) REVERT: A 213 HIS cc_start: 0.7588 (p-80) cc_final: 0.7205 (p-80) REVERT: A 221 ILE cc_start: 0.7609 (mt) cc_final: 0.7155 (mm) REVERT: A 234 LEU cc_start: 0.8250 (tp) cc_final: 0.8050 (mt) REVERT: A 237 ASP cc_start: 0.8032 (t0) cc_final: 0.6503 (p0) REVERT: A 246 SER cc_start: 0.9100 (m) cc_final: 0.8844 (p) REVERT: A 247 MET cc_start: 0.8649 (mtp) cc_final: 0.7707 (mtp) REVERT: A 258 TRP cc_start: 0.7355 (m100) cc_final: 0.7081 (m100) REVERT: A 259 PHE cc_start: 0.7928 (m-80) cc_final: 0.7421 (m-80) REVERT: A 274 PHE cc_start: 0.8083 (t80) cc_final: 0.7534 (t80) REVERT: A 283 LEU cc_start: 0.9490 (mt) cc_final: 0.8935 (pp) REVERT: A 303 ILE cc_start: 0.8946 (mt) cc_final: 0.8474 (mt) REVERT: A 305 CYS cc_start: 0.8215 (m) cc_final: 0.7976 (m) REVERT: A 307 PHE cc_start: 0.8715 (m-80) cc_final: 0.8476 (m-80) REVERT: A 333 GLN cc_start: 0.8733 (mt0) cc_final: 0.8378 (mm-40) REVERT: A 334 PHE cc_start: 0.8955 (t80) cc_final: 0.8710 (t80) REVERT: A 336 PHE cc_start: 0.8050 (t80) cc_final: 0.7811 (t80) REVERT: A 337 ASP cc_start: 0.8421 (m-30) cc_final: 0.7888 (p0) REVERT: A 341 ASP cc_start: 0.8399 (m-30) cc_final: 0.7832 (m-30) REVERT: A 345 LYS cc_start: 0.8704 (mttt) cc_final: 0.8458 (mttt) REVERT: A 346 ASN cc_start: 0.8230 (m-40) cc_final: 0.7923 (t0) REVERT: B 14 LEU cc_start: 0.9172 (mt) cc_final: 0.8737 (mm) REVERT: B 15 LYS cc_start: 0.9010 (mttt) cc_final: 0.8493 (mttt) REVERT: B 19 ARG cc_start: 0.8356 (mtm-85) cc_final: 0.8116 (mtm-85) REVERT: B 23 LYS cc_start: 0.8971 (mtmt) cc_final: 0.8650 (ptpp) REVERT: B 32 GLN cc_start: 0.8302 (mt0) cc_final: 0.7993 (mt0) REVERT: B 81 ILE cc_start: 0.8802 (mm) cc_final: 0.8589 (tp) REVERT: B 89 LYS cc_start: 0.8978 (mttp) cc_final: 0.8753 (mttp) REVERT: B 122 SER cc_start: 0.8792 (m) cc_final: 0.8404 (p) REVERT: B 188 MET cc_start: 0.7722 (mmp) cc_final: 0.7154 (mmm) REVERT: B 209 LYS cc_start: 0.8753 (mttm) cc_final: 0.8536 (mmtp) REVERT: B 217 MET cc_start: 0.7736 (ptm) cc_final: 0.7025 (ptm) REVERT: B 219 ARG cc_start: 0.8286 (mtt-85) cc_final: 0.7665 (mtp85) REVERT: B 256 ARG cc_start: 0.8376 (mtm180) cc_final: 0.7881 (mtm180) REVERT: B 270 ILE cc_start: 0.9382 (pt) cc_final: 0.9174 (mm) REVERT: B 298 ASP cc_start: 0.7816 (t0) cc_final: 0.6966 (p0) REVERT: Y 9 ILE cc_start: 0.6399 (mt) cc_final: 0.5817 (pt) REVERT: Y 22 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8558 (tp30) REVERT: Y 28 ILE cc_start: 0.7454 (pt) cc_final: 0.7209 (pt) REVERT: Y 44 HIS cc_start: 0.8062 (m-70) cc_final: 0.7261 (m-70) REVERT: N 38 ARG cc_start: 0.8434 (ptt180) cc_final: 0.7841 (ptm-80) REVERT: N 102 TYR cc_start: 0.8305 (p90) cc_final: 0.8013 (p90) REVERT: N 109 ASP cc_start: 0.8051 (p0) cc_final: 0.7183 (p0) REVERT: N 160 ARG cc_start: 0.8138 (mtt-85) cc_final: 0.7886 (ttm110) REVERT: C 178 MET cc_start: 0.7777 (mmt) cc_final: 0.7442 (mmm) REVERT: C 189 GLN cc_start: 0.7966 (tt0) cc_final: 0.7489 (tm-30) REVERT: C 200 ASN cc_start: 0.7850 (m-40) cc_final: 0.7495 (m-40) REVERT: C 203 ARG cc_start: 0.8032 (mtt90) cc_final: 0.7798 (mpt-90) REVERT: C 260 TRP cc_start: 0.8188 (m-90) cc_final: 0.7788 (m-90) REVERT: C 279 ARG cc_start: 0.7962 (ttt180) cc_final: 0.7497 (mmm-85) REVERT: C 294 ASN cc_start: 0.7679 (m-40) cc_final: 0.7403 (m-40) REVERT: C 321 SER cc_start: 0.7368 (m) cc_final: 0.7052 (p) REVERT: C 327 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7316 (tm-30) REVERT: C 352 LYS cc_start: 0.8109 (ptpt) cc_final: 0.7565 (mtmm) REVERT: C 379 TYR cc_start: 0.8085 (t80) cc_final: 0.7760 (t80) REVERT: C 380 LYS cc_start: 0.8257 (mtmt) cc_final: 0.7824 (mmmm) REVERT: C 384 PHE cc_start: 0.8717 (p90) cc_final: 0.8507 (p90) REVERT: C 415 MET cc_start: 0.7413 (ttm) cc_final: 0.6907 (ttm) REVERT: C 449 LYS cc_start: 0.8826 (mtmt) cc_final: 0.8505 (mttp) REVERT: C 472 ASP cc_start: 0.7436 (m-30) cc_final: 0.7132 (m-30) REVERT: C 475 TRP cc_start: 0.7199 (m100) cc_final: 0.6788 (m100) REVERT: C 534 MET cc_start: 0.7472 (mtt) cc_final: 0.7065 (mtp) REVERT: C 549 LYS cc_start: 0.8734 (mttp) cc_final: 0.8369 (mtpt) REVERT: C 568 TRP cc_start: 0.8055 (m100) cc_final: 0.6980 (m100) REVERT: C 569 ILE cc_start: 0.8669 (mt) cc_final: 0.8447 (mm) REVERT: C 592 PHE cc_start: 0.7536 (t80) cc_final: 0.7266 (t80) REVERT: C 626 GLN cc_start: 0.6563 (mp10) cc_final: 0.6069 (mp10) REVERT: C 637 CYS cc_start: 0.8230 (m) cc_final: 0.7875 (m) REVERT: C 708 TRP cc_start: 0.6764 (p-90) cc_final: 0.6243 (m100) REVERT: C 745 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7546 (mm-30) REVERT: C 795 SER cc_start: 0.8810 (m) cc_final: 0.8391 (p) REVERT: C 807 MET cc_start: 0.7795 (mtm) cc_final: 0.7589 (mtm) REVERT: C 812 VAL cc_start: 0.8560 (t) cc_final: 0.8286 (p) REVERT: C 853 PHE cc_start: 0.7616 (m-80) cc_final: 0.7377 (m-10) REVERT: D 100 ASP cc_start: 0.6957 (t0) cc_final: 0.6366 (t0) REVERT: D 126 ASN cc_start: 0.6830 (p0) cc_final: 0.6025 (p0) REVERT: D 196 LYS cc_start: 0.8727 (mttt) cc_final: 0.8453 (mmtt) REVERT: D 214 ASP cc_start: 0.7924 (t0) cc_final: 0.7427 (t0) REVERT: D 220 TYR cc_start: 0.8514 (t80) cc_final: 0.8281 (t80) REVERT: D 222 GLU cc_start: 0.8062 (mp0) cc_final: 0.7635 (mp0) REVERT: D 241 LYS cc_start: 0.7572 (mtpt) cc_final: 0.7269 (mmtt) REVERT: D 270 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7890 (mm-30) REVERT: D 288 SER cc_start: 0.8749 (m) cc_final: 0.7737 (p) REVERT: D 311 MET cc_start: 0.7372 (ptp) cc_final: 0.6956 (ptp) REVERT: D 319 PHE cc_start: 0.7483 (p90) cc_final: 0.7190 (p90) REVERT: D 341 GLU cc_start: 0.7568 (pt0) cc_final: 0.7357 (pt0) REVERT: D 342 TYR cc_start: 0.7853 (t80) cc_final: 0.7613 (t80) REVERT: D 418 ARG cc_start: 0.7810 (mtp-110) cc_final: 0.7581 (mtp-110) REVERT: D 427 LYS cc_start: 0.7911 (pttt) cc_final: 0.7558 (ptmm) REVERT: D 467 LYS cc_start: 0.8358 (tppt) cc_final: 0.8116 (tppt) REVERT: D 502 PHE cc_start: 0.7570 (m-10) cc_final: 0.7084 (m-10) REVERT: D 609 LEU cc_start: 0.8098 (tt) cc_final: 0.7824 (mt) REVERT: D 630 MET cc_start: 0.4091 (tmm) cc_final: 0.3860 (tmm) REVERT: D 677 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6744 (tm-30) REVERT: D 744 LEU cc_start: 0.8786 (mp) cc_final: 0.8500 (tt) outliers start: 0 outliers final: 0 residues processed: 701 average time/residue: 0.3779 time to fit residues: 370.3016 Evaluate side-chains 538 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 538 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.6980 chunk 175 optimal weight: 0.0770 chunk 97 optimal weight: 0.0270 chunk 59 optimal weight: 0.0970 chunk 118 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 chunk 209 optimal weight: 0.7980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN Y 11 GLN C 434 ASN ** C 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 HIS ** D 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18896 Z= 0.181 Angle : 0.704 24.489 25600 Z= 0.344 Chirality : 0.060 2.214 2874 Planarity : 0.004 0.083 3237 Dihedral : 5.115 82.641 2548 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.72 % Favored : 97.19 % Rotamer: Outliers : 2.29 % Allowed : 11.57 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2315 helix: 0.50 (0.16), residues: 949 sheet: -0.05 (0.23), residues: 472 loop : -1.02 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.012 0.001 HIS D 393 PHE 0.020 0.001 PHE D 499 TYR 0.023 0.001 TYR D 338 ARG 0.009 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 580 time to evaluate : 2.053 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8971 (mttt) cc_final: 0.8534 (mtmm) REVERT: A 24 ARG cc_start: 0.8162 (ttt-90) cc_final: 0.7919 (ttt-90) REVERT: A 25 GLU cc_start: 0.8343 (tt0) cc_final: 0.8095 (tt0) REVERT: A 29 LYS cc_start: 0.8275 (tmtt) cc_final: 0.7662 (tmtt) REVERT: A 76 ASN cc_start: 0.7416 (m-40) cc_final: 0.7005 (t0) REVERT: A 154 TYR cc_start: 0.8192 (m-80) cc_final: 0.7875 (m-80) REVERT: A 192 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8387 (ptmm) REVERT: A 194 LEU cc_start: 0.8047 (mp) cc_final: 0.7748 (tp) REVERT: A 196 PHE cc_start: 0.8754 (m-80) cc_final: 0.8427 (m-80) REVERT: A 246 SER cc_start: 0.9116 (m) cc_final: 0.8796 (p) REVERT: A 274 PHE cc_start: 0.7914 (t80) cc_final: 0.7386 (t80) REVERT: A 283 LEU cc_start: 0.9437 (mt) cc_final: 0.8834 (pp) REVERT: A 287 TYR cc_start: 0.7927 (m-80) cc_final: 0.7686 (m-80) REVERT: A 303 ILE cc_start: 0.8918 (mt) cc_final: 0.8549 (pt) REVERT: A 304 GLN cc_start: 0.8232 (tt0) cc_final: 0.7876 (tp40) REVERT: A 313 ARG cc_start: 0.8221 (ttm110) cc_final: 0.7894 (ttp-170) REVERT: A 320 TYR cc_start: 0.7293 (m-80) cc_final: 0.7052 (m-80) REVERT: A 333 GLN cc_start: 0.8776 (mt0) cc_final: 0.8435 (mm-40) REVERT: A 334 PHE cc_start: 0.8923 (t80) cc_final: 0.8503 (t80) REVERT: A 336 PHE cc_start: 0.8365 (t80) cc_final: 0.7473 (t80) REVERT: A 337 ASP cc_start: 0.8337 (m-30) cc_final: 0.7783 (p0) REVERT: A 341 ASP cc_start: 0.8357 (m-30) cc_final: 0.7887 (m-30) REVERT: A 343 ILE cc_start: 0.7703 (mt) cc_final: 0.7444 (mt) REVERT: A 346 ASN cc_start: 0.8200 (m-40) cc_final: 0.7919 (m-40) REVERT: B 9 GLN cc_start: 0.8836 (mt0) cc_final: 0.8580 (mt0) REVERT: B 12 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8394 (pp20) REVERT: B 15 LYS cc_start: 0.8935 (mttt) cc_final: 0.8543 (mttt) REVERT: B 19 ARG cc_start: 0.8555 (mtm-85) cc_final: 0.8246 (mtm-85) REVERT: B 42 ARG cc_start: 0.8184 (tmm-80) cc_final: 0.7951 (tmm-80) REVERT: B 44 GLN cc_start: 0.8303 (mt0) cc_final: 0.7990 (mt0) REVERT: B 122 SER cc_start: 0.8863 (m) cc_final: 0.8515 (p) REVERT: B 252 LEU cc_start: 0.7945 (tp) cc_final: 0.7633 (tp) REVERT: B 256 ARG cc_start: 0.8369 (mtm180) cc_final: 0.7832 (mtm180) REVERT: B 262 MET cc_start: 0.8026 (mmm) cc_final: 0.7715 (mmp) REVERT: B 298 ASP cc_start: 0.7757 (t0) cc_final: 0.7415 (t70) REVERT: Y 9 ILE cc_start: 0.6413 (mt) cc_final: 0.5875 (pt) REVERT: Y 14 LYS cc_start: 0.8738 (mppt) cc_final: 0.8440 (mppt) REVERT: Y 18 GLN cc_start: 0.8573 (tp40) cc_final: 0.7303 (tp40) REVERT: Y 21 MET cc_start: 0.8390 (tmm) cc_final: 0.5701 (tmm) REVERT: Y 22 GLU cc_start: 0.8707 (mt-10) cc_final: 0.7850 (mm-30) REVERT: Y 28 ILE cc_start: 0.7561 (pt) cc_final: 0.7328 (pt) REVERT: Y 32 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7642 (mmtt) REVERT: Y 44 HIS cc_start: 0.7803 (m-70) cc_final: 0.7599 (m-70) REVERT: N 96 CYS cc_start: 0.7293 (p) cc_final: 0.6599 (p) REVERT: N 98 ARG cc_start: 0.7813 (ttt180) cc_final: 0.7567 (ptt180) REVERT: N 110 PHE cc_start: 0.8631 (t80) cc_final: 0.8412 (t80) REVERT: N 160 ARG cc_start: 0.8151 (mtt-85) cc_final: 0.7912 (ttm110) REVERT: N 189 ILE cc_start: 0.8229 (mp) cc_final: 0.7926 (mm) REVERT: C 178 MET cc_start: 0.7313 (mmt) cc_final: 0.7019 (mmm) REVERT: C 200 ASN cc_start: 0.7811 (m-40) cc_final: 0.7441 (m-40) REVERT: C 255 GLU cc_start: 0.8340 (tp30) cc_final: 0.7724 (tp30) REVERT: C 260 TRP cc_start: 0.8216 (m-90) cc_final: 0.7933 (m-90) REVERT: C 279 ARG cc_start: 0.8055 (ttt180) cc_final: 0.7682 (mmm-85) REVERT: C 294 ASN cc_start: 0.7996 (m-40) cc_final: 0.7751 (m-40) REVERT: C 321 SER cc_start: 0.7398 (m) cc_final: 0.7040 (p) REVERT: C 327 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7534 (tm-30) REVERT: C 379 TYR cc_start: 0.7936 (t80) cc_final: 0.7475 (t80) REVERT: C 380 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7681 (mmmm) REVERT: C 415 MET cc_start: 0.7361 (ttm) cc_final: 0.6983 (ttm) REVERT: C 448 GLU cc_start: 0.8576 (pt0) cc_final: 0.8095 (pt0) REVERT: C 452 LYS cc_start: 0.9146 (mtpp) cc_final: 0.8695 (mtmm) REVERT: C 454 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8664 (mm) REVERT: C 456 ARG cc_start: 0.7666 (mtm180) cc_final: 0.7254 (mtm110) REVERT: C 472 ASP cc_start: 0.7716 (m-30) cc_final: 0.7427 (m-30) REVERT: C 483 LYS cc_start: 0.8546 (tmtt) cc_final: 0.8272 (tppt) REVERT: C 548 LYS cc_start: 0.8305 (mmmt) cc_final: 0.7973 (mmmt) REVERT: C 567 LYS cc_start: 0.7825 (ttpp) cc_final: 0.7567 (ttpp) REVERT: C 621 TYR cc_start: 0.7176 (p90) cc_final: 0.6809 (p90) REVERT: C 623 GLN cc_start: 0.7871 (pt0) cc_final: 0.7459 (mt0) REVERT: C 626 GLN cc_start: 0.6637 (mp10) cc_final: 0.6165 (mp10) REVERT: C 637 CYS cc_start: 0.8185 (m) cc_final: 0.7832 (m) REVERT: C 708 TRP cc_start: 0.6758 (p-90) cc_final: 0.6233 (m100) REVERT: C 792 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8506 (pttt) REVERT: C 795 SER cc_start: 0.8766 (m) cc_final: 0.8398 (p) REVERT: C 807 MET cc_start: 0.7714 (mtm) cc_final: 0.7510 (mtm) REVERT: C 812 VAL cc_start: 0.8542 (t) cc_final: 0.8293 (p) REVERT: C 814 VAL cc_start: 0.8211 (OUTLIER) cc_final: 0.7980 (p) REVERT: C 847 ILE cc_start: 0.8560 (mm) cc_final: 0.8343 (mt) REVERT: D 94 LEU cc_start: 0.8120 (mm) cc_final: 0.7776 (pt) REVERT: D 112 LYS cc_start: 0.8336 (mtpp) cc_final: 0.7881 (ttmm) REVERT: D 126 ASN cc_start: 0.6854 (p0) cc_final: 0.6041 (p0) REVERT: D 214 ASP cc_start: 0.7775 (t0) cc_final: 0.7150 (t0) REVERT: D 220 TYR cc_start: 0.8498 (t80) cc_final: 0.8245 (t80) REVERT: D 222 GLU cc_start: 0.7951 (mp0) cc_final: 0.7591 (mp0) REVERT: D 226 ILE cc_start: 0.8431 (mt) cc_final: 0.8110 (tp) REVERT: D 268 TYR cc_start: 0.8124 (t80) cc_final: 0.7881 (t80) REVERT: D 288 SER cc_start: 0.8736 (m) cc_final: 0.8185 (p) REVERT: D 311 MET cc_start: 0.7497 (ptp) cc_final: 0.7118 (ptp) REVERT: D 338 TYR cc_start: 0.7450 (t80) cc_final: 0.6920 (t80) REVERT: D 342 TYR cc_start: 0.8016 (t80) cc_final: 0.7056 (t80) REVERT: D 398 ILE cc_start: 0.9002 (mt) cc_final: 0.8727 (mm) REVERT: D 415 VAL cc_start: 0.8621 (t) cc_final: 0.8182 (m) REVERT: D 476 LYS cc_start: 0.8305 (ptmm) cc_final: 0.8039 (ptmm) REVERT: D 579 HIS cc_start: 0.8503 (t-90) cc_final: 0.8184 (t-170) REVERT: D 609 LEU cc_start: 0.8123 (tt) cc_final: 0.7875 (mt) REVERT: D 697 TYR cc_start: 0.7963 (t80) cc_final: 0.7699 (t80) REVERT: D 744 LEU cc_start: 0.8808 (mp) cc_final: 0.8099 (tt) outliers start: 46 outliers final: 25 residues processed: 599 average time/residue: 0.3741 time to fit residues: 318.8941 Evaluate side-chains 551 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 523 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 502 ASN Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 792 LYS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 519 MET Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 674 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 210 optimal weight: 0.3980 chunk 227 optimal weight: 0.3980 chunk 187 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 168 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Y 11 GLN C 514 ASN C 623 GLN C 628 ASN D 192 HIS D 393 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18896 Z= 0.202 Angle : 0.690 26.397 25600 Z= 0.337 Chirality : 0.057 1.975 2874 Planarity : 0.004 0.045 3237 Dihedral : 5.026 80.181 2548 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 3.13 % Allowed : 14.51 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2315 helix: 0.65 (0.17), residues: 947 sheet: 0.11 (0.24), residues: 465 loop : -0.85 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS D 393 PHE 0.037 0.002 PHE A 307 TYR 0.021 0.001 TYR D 663 ARG 0.007 0.001 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 548 time to evaluate : 1.810 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8684 (m-30) cc_final: 0.8332 (m-30) REVERT: A 10 LYS cc_start: 0.9004 (mttt) cc_final: 0.8510 (mtmm) REVERT: A 29 LYS cc_start: 0.8469 (tmtt) cc_final: 0.8254 (tmtt) REVERT: A 32 ARG cc_start: 0.7393 (mpt-90) cc_final: 0.7156 (mpt-90) REVERT: A 154 TYR cc_start: 0.8200 (m-80) cc_final: 0.7575 (m-80) REVERT: A 194 LEU cc_start: 0.8194 (mp) cc_final: 0.7930 (tp) REVERT: A 232 LEU cc_start: 0.8316 (tp) cc_final: 0.8028 (tp) REVERT: A 236 GLU cc_start: 0.8943 (mp0) cc_final: 0.8372 (mp0) REVERT: A 237 ASP cc_start: 0.8650 (m-30) cc_final: 0.7397 (p0) REVERT: A 242 ARG cc_start: 0.7574 (mmm160) cc_final: 0.7325 (mmm-85) REVERT: A 246 SER cc_start: 0.9067 (m) cc_final: 0.8729 (p) REVERT: A 274 PHE cc_start: 0.7889 (t80) cc_final: 0.7289 (t80) REVERT: A 283 LEU cc_start: 0.9457 (mt) cc_final: 0.8938 (pp) REVERT: A 287 TYR cc_start: 0.8358 (m-80) cc_final: 0.7869 (m-80) REVERT: A 303 ILE cc_start: 0.9021 (mt) cc_final: 0.8709 (mt) REVERT: A 307 PHE cc_start: 0.8701 (m-80) cc_final: 0.8403 (m-80) REVERT: A 313 ARG cc_start: 0.8671 (ttm110) cc_final: 0.8102 (ttp-170) REVERT: A 328 ASP cc_start: 0.6883 (t0) cc_final: 0.6275 (t0) REVERT: A 333 GLN cc_start: 0.8776 (mt0) cc_final: 0.8537 (mm-40) REVERT: A 334 PHE cc_start: 0.8864 (t80) cc_final: 0.8589 (t80) REVERT: A 341 ASP cc_start: 0.8429 (m-30) cc_final: 0.8087 (m-30) REVERT: A 345 LYS cc_start: 0.8755 (ptpt) cc_final: 0.8544 (ptpp) REVERT: A 346 ASN cc_start: 0.8130 (m-40) cc_final: 0.7822 (m-40) REVERT: B 15 LYS cc_start: 0.8951 (mttt) cc_final: 0.8587 (mttt) REVERT: B 19 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.8280 (mtm-85) REVERT: B 23 LYS cc_start: 0.9026 (mtmt) cc_final: 0.8737 (mttp) REVERT: B 52 ARG cc_start: 0.8057 (mtp85) cc_final: 0.7687 (ptp90) REVERT: B 122 SER cc_start: 0.8858 (m) cc_final: 0.8494 (p) REVERT: B 154 ASP cc_start: 0.8169 (t0) cc_final: 0.7896 (t0) REVERT: B 209 LYS cc_start: 0.8601 (mttm) cc_final: 0.8355 (mmtp) REVERT: B 256 ARG cc_start: 0.8253 (mtm180) cc_final: 0.7735 (mtm180) REVERT: B 298 ASP cc_start: 0.7803 (t0) cc_final: 0.7463 (t70) REVERT: Y 14 LYS cc_start: 0.8663 (mppt) cc_final: 0.8383 (mmtm) REVERT: Y 18 GLN cc_start: 0.8702 (tp40) cc_final: 0.8179 (tp40) REVERT: Y 22 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8328 (mm-30) REVERT: Y 28 ILE cc_start: 0.7833 (pt) cc_final: 0.7608 (pt) REVERT: Y 32 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7813 (mmtt) REVERT: N 94 TYR cc_start: 0.8128 (m-10) cc_final: 0.7914 (m-80) REVERT: N 110 PHE cc_start: 0.8741 (t80) cc_final: 0.8496 (t80) REVERT: C 255 GLU cc_start: 0.8414 (tp30) cc_final: 0.7975 (tp30) REVERT: C 279 ARG cc_start: 0.8091 (ttt180) cc_final: 0.7766 (mmm-85) REVERT: C 321 SER cc_start: 0.7381 (m) cc_final: 0.6987 (p) REVERT: C 327 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7669 (tm-30) REVERT: C 356 ARG cc_start: 0.7641 (ttp-170) cc_final: 0.7374 (ttp-170) REVERT: C 379 TYR cc_start: 0.8075 (t80) cc_final: 0.7581 (t80) REVERT: C 380 LYS cc_start: 0.8278 (mtmt) cc_final: 0.8040 (mtmt) REVERT: C 415 MET cc_start: 0.7490 (ttm) cc_final: 0.7128 (ttm) REVERT: C 449 LYS cc_start: 0.8909 (mtmt) cc_final: 0.8514 (mtpt) REVERT: C 454 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8612 (mm) REVERT: C 457 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.7431 (t-90) REVERT: C 483 LYS cc_start: 0.8644 (tmtt) cc_final: 0.8422 (tppt) REVERT: C 503 GLN cc_start: 0.8075 (mp10) cc_final: 0.7466 (tm-30) REVERT: C 511 ARG cc_start: 0.6492 (mmp-170) cc_final: 0.6274 (mmp-170) REVERT: C 548 LYS cc_start: 0.8370 (mmmt) cc_final: 0.8066 (mmmt) REVERT: C 567 LYS cc_start: 0.8157 (ttpp) cc_final: 0.7835 (ttpp) REVERT: C 623 GLN cc_start: 0.7663 (pt0) cc_final: 0.7123 (pm20) REVERT: C 626 GLN cc_start: 0.7017 (mp10) cc_final: 0.6504 (mp10) REVERT: C 637 CYS cc_start: 0.7975 (m) cc_final: 0.7713 (m) REVERT: C 708 TRP cc_start: 0.6857 (p-90) cc_final: 0.6261 (m100) REVERT: C 795 SER cc_start: 0.8891 (m) cc_final: 0.8504 (p) REVERT: C 812 VAL cc_start: 0.8578 (t) cc_final: 0.8331 (p) REVERT: C 847 ILE cc_start: 0.8582 (mm) cc_final: 0.8336 (mt) REVERT: D 62 MET cc_start: 0.7924 (ptm) cc_final: 0.7533 (tmm) REVERT: D 95 ARG cc_start: 0.7701 (tpp80) cc_final: 0.7455 (mmm160) REVERT: D 112 LYS cc_start: 0.8243 (mtpp) cc_final: 0.7857 (mtpt) REVERT: D 126 ASN cc_start: 0.7097 (p0) cc_final: 0.6319 (p0) REVERT: D 222 GLU cc_start: 0.7987 (mp0) cc_final: 0.7701 (mp0) REVERT: D 223 ASP cc_start: 0.7696 (p0) cc_final: 0.7471 (p0) REVERT: D 226 ILE cc_start: 0.8517 (mt) cc_final: 0.7684 (tp) REVERT: D 272 MET cc_start: 0.7839 (ttt) cc_final: 0.7504 (mtt) REVERT: D 311 MET cc_start: 0.7654 (ptp) cc_final: 0.7288 (ptp) REVERT: D 342 TYR cc_start: 0.8095 (t80) cc_final: 0.7849 (t80) REVERT: D 397 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7375 (mmm160) REVERT: D 421 GLU cc_start: 0.7135 (tp30) cc_final: 0.6703 (tp30) REVERT: D 476 LYS cc_start: 0.8314 (ptmm) cc_final: 0.8104 (pptt) REVERT: D 678 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7710 (t) REVERT: D 697 TYR cc_start: 0.8088 (t80) cc_final: 0.7848 (t80) outliers start: 63 outliers final: 38 residues processed: 580 average time/residue: 0.3616 time to fit residues: 298.7181 Evaluate side-chains 551 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 510 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 194 ASN Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 502 ASN Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 615 TYR Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 645 PHE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 501 PHE Chi-restraints excluded: chain D residue 608 ASP Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 678 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 0.0970 chunk 158 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 223 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 199 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 9 GLN B 44 GLN ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18896 Z= 0.198 Angle : 0.693 25.623 25600 Z= 0.335 Chirality : 0.058 2.050 2874 Planarity : 0.004 0.082 3237 Dihedral : 4.976 77.267 2548 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.98 % Favored : 96.98 % Rotamer: Outliers : 3.68 % Allowed : 17.09 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 2315 helix: 0.65 (0.17), residues: 955 sheet: 0.24 (0.24), residues: 462 loop : -0.89 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 562 HIS 0.004 0.001 HIS C 689 PHE 0.023 0.001 PHE C 446 TYR 0.029 0.001 TYR D 663 ARG 0.010 0.001 ARG Y 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 519 time to evaluate : 2.166 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: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8657 (m-30) cc_final: 0.8191 (m-30) REVERT: A 10 LYS cc_start: 0.9005 (mttt) cc_final: 0.8509 (mtmm) REVERT: A 26 ASP cc_start: 0.8676 (t0) cc_final: 0.7960 (m-30) REVERT: A 29 LYS cc_start: 0.8545 (tmtt) cc_final: 0.8170 (tmtt) REVERT: A 32 ARG cc_start: 0.7396 (mpt-90) cc_final: 0.7169 (mpt-90) REVERT: A 154 TYR cc_start: 0.7951 (m-80) cc_final: 0.7550 (m-80) REVERT: A 158 ASP cc_start: 0.7252 (t0) cc_final: 0.7003 (t0) REVERT: A 191 PHE cc_start: 0.7944 (t80) cc_final: 0.7543 (t80) REVERT: A 194 LEU cc_start: 0.8290 (mp) cc_final: 0.8065 (tp) REVERT: A 234 LEU cc_start: 0.8912 (mt) cc_final: 0.8674 (mt) REVERT: A 237 ASP cc_start: 0.8726 (m-30) cc_final: 0.7496 (p0) REVERT: A 246 SER cc_start: 0.9074 (m) cc_final: 0.8741 (p) REVERT: A 274 PHE cc_start: 0.7893 (t80) cc_final: 0.7264 (t80) REVERT: A 283 LEU cc_start: 0.9465 (mt) cc_final: 0.8908 (pp) REVERT: A 287 TYR cc_start: 0.8349 (m-80) cc_final: 0.7881 (m-80) REVERT: A 303 ILE cc_start: 0.9027 (mt) cc_final: 0.8366 (tp) REVERT: A 307 PHE cc_start: 0.8674 (m-80) cc_final: 0.8266 (m-80) REVERT: A 313 ARG cc_start: 0.8820 (ttm110) cc_final: 0.8375 (ttp-170) REVERT: A 334 PHE cc_start: 0.8841 (t80) cc_final: 0.8574 (t80) REVERT: A 346 ASN cc_start: 0.8168 (m-40) cc_final: 0.7875 (m-40) REVERT: B 9 GLN cc_start: 0.8874 (mt0) cc_final: 0.8504 (mt0) REVERT: B 12 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8462 (pp20) REVERT: B 15 LYS cc_start: 0.8980 (mttt) cc_final: 0.8569 (mttt) REVERT: B 19 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.8239 (mtm-85) REVERT: B 23 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8738 (mttt) REVERT: B 52 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7675 (ptp90) REVERT: B 101 MET cc_start: 0.8004 (mmm) cc_final: 0.7730 (tpp) REVERT: B 122 SER cc_start: 0.8864 (m) cc_final: 0.8483 (p) REVERT: B 154 ASP cc_start: 0.8133 (t0) cc_final: 0.7773 (t0) REVERT: B 175 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8490 (tm-30) REVERT: B 209 LYS cc_start: 0.8601 (mttm) cc_final: 0.8382 (mmtp) REVERT: B 289 TYR cc_start: 0.6875 (m-80) cc_final: 0.6062 (m-80) REVERT: B 298 ASP cc_start: 0.7756 (t0) cc_final: 0.7447 (t70) REVERT: Y 18 GLN cc_start: 0.8766 (tp40) cc_final: 0.8147 (tm-30) REVERT: Y 21 MET cc_start: 0.8519 (tmm) cc_final: 0.7894 (tmm) REVERT: Y 32 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7931 (mmtt) REVERT: N 94 TYR cc_start: 0.8202 (m-10) cc_final: 0.7901 (m-80) REVERT: N 110 PHE cc_start: 0.8746 (t80) cc_final: 0.8458 (t80) REVERT: N 219 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8519 (tp) REVERT: C 197 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7646 (mm-30) REVERT: C 255 GLU cc_start: 0.8437 (tp30) cc_final: 0.8214 (tp30) REVERT: C 279 ARG cc_start: 0.8098 (ttt180) cc_final: 0.7821 (mmm-85) REVERT: C 321 SER cc_start: 0.7336 (m) cc_final: 0.6918 (p) REVERT: C 327 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7712 (tm-30) REVERT: C 379 TYR cc_start: 0.8075 (t80) cc_final: 0.7532 (t80) REVERT: C 380 LYS cc_start: 0.8235 (mtmt) cc_final: 0.7792 (mmmm) REVERT: C 399 ASN cc_start: 0.8127 (p0) cc_final: 0.7530 (p0) REVERT: C 415 MET cc_start: 0.7497 (ttm) cc_final: 0.7128 (ttm) REVERT: C 449 LYS cc_start: 0.8986 (mtmt) cc_final: 0.8691 (ttmt) REVERT: C 454 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8557 (mm) REVERT: C 457 HIS cc_start: 0.7755 (OUTLIER) cc_final: 0.7418 (t-90) REVERT: C 503 GLN cc_start: 0.8149 (mp10) cc_final: 0.7514 (tm-30) REVERT: C 534 MET cc_start: 0.7291 (mtp) cc_final: 0.7044 (mtp) REVERT: C 548 LYS cc_start: 0.8375 (mmmt) cc_final: 0.8099 (mmmt) REVERT: C 557 LYS cc_start: 0.8424 (mtpt) cc_final: 0.8132 (mtmm) REVERT: C 559 ASP cc_start: 0.7550 (t0) cc_final: 0.7304 (m-30) REVERT: C 567 LYS cc_start: 0.8262 (ttpp) cc_final: 0.7864 (ttpp) REVERT: C 568 TRP cc_start: 0.7941 (m100) cc_final: 0.7257 (m100) REVERT: C 626 GLN cc_start: 0.7114 (mp10) cc_final: 0.6819 (mp10) REVERT: C 708 TRP cc_start: 0.6922 (p-90) cc_final: 0.6305 (m100) REVERT: C 795 SER cc_start: 0.8891 (m) cc_final: 0.8514 (p) REVERT: C 807 MET cc_start: 0.7721 (mtm) cc_final: 0.7172 (mtm) REVERT: C 812 VAL cc_start: 0.8563 (t) cc_final: 0.8312 (p) REVERT: D 62 MET cc_start: 0.7923 (ptm) cc_final: 0.7561 (tmm) REVERT: D 95 ARG cc_start: 0.7776 (tpp80) cc_final: 0.7546 (mmm160) REVERT: D 107 GLU cc_start: 0.7252 (mp0) cc_final: 0.5947 (mp0) REVERT: D 112 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7662 (mtpt) REVERT: D 126 ASN cc_start: 0.7018 (p0) cc_final: 0.6289 (p0) REVERT: D 144 GLU cc_start: 0.7405 (tt0) cc_final: 0.7120 (tp30) REVERT: D 174 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8154 (ttp-110) REVERT: D 222 GLU cc_start: 0.7993 (mp0) cc_final: 0.7759 (mp0) REVERT: D 272 MET cc_start: 0.7945 (ttt) cc_final: 0.7601 (mtt) REVERT: D 311 MET cc_start: 0.7730 (ptp) cc_final: 0.7381 (ptp) REVERT: D 342 TYR cc_start: 0.8224 (t80) cc_final: 0.7951 (t80) REVERT: D 397 ARG cc_start: 0.7840 (mmm160) cc_final: 0.7127 (mmm160) REVERT: D 626 GLU cc_start: 0.7537 (pt0) cc_final: 0.7090 (pp20) REVERT: D 678 THR cc_start: 0.8152 (OUTLIER) cc_final: 0.7794 (t) outliers start: 74 outliers final: 48 residues processed: 559 average time/residue: 0.3894 time to fit residues: 310.2269 Evaluate side-chains 557 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 504 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 194 ASN Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 502 ASN Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 615 TYR Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 645 PHE Chi-restraints excluded: chain C residue 663 CYS Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 824 MET Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 174 ARG Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 608 ASP Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 741 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 166 optimal weight: 0.0270 chunk 92 optimal weight: 10.0000 chunk 190 optimal weight: 0.0470 chunk 154 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 200 optimal weight: 0.0980 chunk 56 optimal weight: 0.2980 overall best weight: 0.1114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN B 237 ASN Y 11 GLN C 628 ASN D 337 GLN D 393 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18896 Z= 0.168 Angle : 0.701 25.969 25600 Z= 0.335 Chirality : 0.056 2.011 2874 Planarity : 0.004 0.086 3237 Dihedral : 4.812 75.440 2548 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 2.83 % Allowed : 18.38 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2315 helix: 0.69 (0.17), residues: 946 sheet: 0.23 (0.23), residues: 479 loop : -0.83 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 562 HIS 0.003 0.001 HIS C 618 PHE 0.027 0.001 PHE D 499 TYR 0.030 0.001 TYR D 390 ARG 0.011 0.001 ARG Y 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 529 time to evaluate : 2.105 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 9 ASP cc_start: 0.8604 (m-30) cc_final: 0.8136 (m-30) REVERT: A 10 LYS cc_start: 0.8958 (mttt) cc_final: 0.8445 (mtmm) REVERT: A 21 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7811 (ttp80) REVERT: A 26 ASP cc_start: 0.8289 (t0) cc_final: 0.7945 (m-30) REVERT: A 29 LYS cc_start: 0.8583 (tmtt) cc_final: 0.8227 (tmtt) REVERT: A 32 ARG cc_start: 0.7393 (mpt-90) cc_final: 0.7135 (mpt-90) REVERT: A 129 ARG cc_start: 0.7284 (tpm170) cc_final: 0.7024 (tpm170) REVERT: A 154 TYR cc_start: 0.7870 (m-80) cc_final: 0.7457 (m-80) REVERT: A 158 ASP cc_start: 0.7489 (t0) cc_final: 0.7247 (t0) REVERT: A 189 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.6355 (t80) REVERT: A 194 LEU cc_start: 0.8290 (mp) cc_final: 0.7928 (tp) REVERT: A 198 MET cc_start: 0.8304 (ttm) cc_final: 0.8045 (tpp) REVERT: A 246 SER cc_start: 0.9058 (m) cc_final: 0.8731 (p) REVERT: A 274 PHE cc_start: 0.7747 (t80) cc_final: 0.7153 (t80) REVERT: A 283 LEU cc_start: 0.9449 (mt) cc_final: 0.8854 (pp) REVERT: A 287 TYR cc_start: 0.8278 (m-80) cc_final: 0.7804 (m-80) REVERT: A 303 ILE cc_start: 0.8941 (mt) cc_final: 0.8526 (pt) REVERT: A 313 ARG cc_start: 0.8746 (ttm110) cc_final: 0.8506 (ttp-170) REVERT: A 328 ASP cc_start: 0.6748 (t0) cc_final: 0.6124 (t0) REVERT: A 334 PHE cc_start: 0.8789 (t80) cc_final: 0.8493 (t80) REVERT: A 337 ASP cc_start: 0.8131 (m-30) cc_final: 0.7711 (m-30) REVERT: A 346 ASN cc_start: 0.8172 (m-40) cc_final: 0.7856 (m-40) REVERT: B 15 LYS cc_start: 0.8993 (mttt) cc_final: 0.8509 (mttt) REVERT: B 19 ARG cc_start: 0.8437 (mtm-85) cc_final: 0.8201 (mtm-85) REVERT: B 23 LYS cc_start: 0.9032 (mtmt) cc_final: 0.8798 (mttt) REVERT: B 52 ARG cc_start: 0.8039 (mtp85) cc_final: 0.7813 (ptp90) REVERT: B 101 MET cc_start: 0.8006 (mmm) cc_final: 0.7723 (tpp) REVERT: B 130 GLU cc_start: 0.7797 (mp0) cc_final: 0.7429 (mp0) REVERT: B 154 ASP cc_start: 0.8082 (t0) cc_final: 0.7766 (t0) REVERT: B 289 TYR cc_start: 0.6812 (m-80) cc_final: 0.5986 (m-80) REVERT: B 298 ASP cc_start: 0.7692 (t0) cc_final: 0.7385 (t70) REVERT: Y 14 LYS cc_start: 0.8643 (mppt) cc_final: 0.8422 (mmtm) REVERT: Y 32 LYS cc_start: 0.8274 (mmtt) cc_final: 0.7898 (mmtt) REVERT: N 110 PHE cc_start: 0.8733 (t80) cc_final: 0.8419 (t80) REVERT: N 179 GLN cc_start: 0.7732 (tm-30) cc_final: 0.7471 (tm-30) REVERT: N 195 LEU cc_start: 0.9336 (mt) cc_final: 0.9075 (tp) REVERT: N 219 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8493 (tp) REVERT: N 230 MET cc_start: 0.7131 (ttp) cc_final: 0.6807 (tmm) REVERT: C 178 MET cc_start: 0.8356 (mmm) cc_final: 0.8002 (mmm) REVERT: C 197 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7713 (mm-30) REVERT: C 255 GLU cc_start: 0.8348 (tp30) cc_final: 0.8124 (tp30) REVERT: C 279 ARG cc_start: 0.8060 (ttt180) cc_final: 0.7833 (mmm-85) REVERT: C 321 SER cc_start: 0.7303 (m) cc_final: 0.6912 (p) REVERT: C 327 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7790 (tm-30) REVERT: C 357 GLN cc_start: 0.8209 (tp40) cc_final: 0.7414 (tm-30) REVERT: C 375 PHE cc_start: 0.8608 (m-80) cc_final: 0.8179 (m-80) REVERT: C 379 TYR cc_start: 0.7977 (t80) cc_final: 0.7496 (t80) REVERT: C 388 TYR cc_start: 0.8183 (m-80) cc_final: 0.7886 (m-10) REVERT: C 415 MET cc_start: 0.7452 (ttm) cc_final: 0.7118 (ttm) REVERT: C 449 LYS cc_start: 0.8928 (mtmt) cc_final: 0.8697 (ttmt) REVERT: C 454 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8570 (mm) REVERT: C 457 HIS cc_start: 0.7700 (OUTLIER) cc_final: 0.7416 (t-90) REVERT: C 472 ASP cc_start: 0.7868 (m-30) cc_final: 0.7549 (m-30) REVERT: C 483 LYS cc_start: 0.8642 (tmtt) cc_final: 0.8282 (mtmm) REVERT: C 548 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8057 (mmmt) REVERT: C 559 ASP cc_start: 0.7466 (t0) cc_final: 0.7005 (t0) REVERT: C 567 LYS cc_start: 0.8192 (ttpp) cc_final: 0.7812 (ttpp) REVERT: C 610 LEU cc_start: 0.6979 (mt) cc_final: 0.6497 (mt) REVERT: C 626 GLN cc_start: 0.7150 (mp10) cc_final: 0.6830 (mp10) REVERT: C 708 TRP cc_start: 0.6893 (p-90) cc_final: 0.6305 (m100) REVERT: C 743 LYS cc_start: 0.8224 (tmtt) cc_final: 0.7960 (tmtt) REVERT: C 795 SER cc_start: 0.8806 (m) cc_final: 0.8444 (p) REVERT: C 812 VAL cc_start: 0.8461 (t) cc_final: 0.8201 (p) REVERT: D 62 MET cc_start: 0.7850 (ptm) cc_final: 0.7528 (tmm) REVERT: D 95 ARG cc_start: 0.7792 (tpp80) cc_final: 0.7499 (mmm160) REVERT: D 107 GLU cc_start: 0.7188 (mp0) cc_final: 0.6624 (mp0) REVERT: D 112 LYS cc_start: 0.8218 (mtpp) cc_final: 0.7759 (mtpt) REVERT: D 126 ASN cc_start: 0.6874 (p0) cc_final: 0.6179 (p0) REVERT: D 222 GLU cc_start: 0.7922 (mp0) cc_final: 0.7702 (mp0) REVERT: D 276 LYS cc_start: 0.8338 (ptmt) cc_final: 0.8134 (ptmt) REVERT: D 311 MET cc_start: 0.7687 (ptp) cc_final: 0.7311 (ptp) REVERT: D 319 PHE cc_start: 0.7554 (p90) cc_final: 0.7318 (p90) REVERT: D 353 LYS cc_start: 0.8984 (mmtm) cc_final: 0.8747 (mmmt) REVERT: D 397 ARG cc_start: 0.7888 (mmm160) cc_final: 0.7154 (mmm160) REVERT: D 432 GLN cc_start: 0.8663 (mt0) cc_final: 0.8213 (mm-40) REVERT: D 493 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6660 (mmm) REVERT: D 528 MET cc_start: 0.6927 (mmp) cc_final: 0.6304 (mmp) REVERT: D 579 HIS cc_start: 0.8462 (t-90) cc_final: 0.8253 (t-90) REVERT: D 626 GLU cc_start: 0.7450 (pt0) cc_final: 0.7013 (pp20) REVERT: D 678 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7815 (t) outliers start: 57 outliers final: 34 residues processed: 557 average time/residue: 0.3720 time to fit residues: 295.2782 Evaluate side-chains 536 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 496 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain Y residue 11 GLN Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 159 CYS Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 502 ASN Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 645 PHE Chi-restraints excluded: chain C residue 663 CYS Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 608 ASP Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 678 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 223 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 GLN ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 18896 Z= 0.261 Angle : 0.752 26.344 25600 Z= 0.365 Chirality : 0.057 1.922 2874 Planarity : 0.004 0.040 3237 Dihedral : 4.945 76.654 2548 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.54 % Favored : 96.41 % Rotamer: Outliers : 3.73 % Allowed : 18.98 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2315 helix: 0.67 (0.17), residues: 960 sheet: 0.30 (0.23), residues: 485 loop : -0.87 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 562 HIS 0.006 0.001 HIS C 689 PHE 0.042 0.002 PHE D 499 TYR 0.027 0.002 TYR D 338 ARG 0.008 0.001 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 517 time to evaluate : 2.282 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 9 ASP cc_start: 0.8617 (m-30) cc_final: 0.8141 (m-30) REVERT: A 10 LYS cc_start: 0.8962 (mttt) cc_final: 0.8437 (mtmm) REVERT: A 29 LYS cc_start: 0.8643 (tmtt) cc_final: 0.8202 (tmtt) REVERT: A 32 ARG cc_start: 0.7418 (mpt-90) cc_final: 0.7097 (mpt-90) REVERT: A 129 ARG cc_start: 0.7420 (tpm170) cc_final: 0.7171 (tpm170) REVERT: A 154 TYR cc_start: 0.7932 (m-80) cc_final: 0.7520 (m-80) REVERT: A 189 PHE cc_start: 0.6714 (OUTLIER) cc_final: 0.6360 (t80) REVERT: A 194 LEU cc_start: 0.8390 (mp) cc_final: 0.7990 (tp) REVERT: A 198 MET cc_start: 0.8348 (ttm) cc_final: 0.8134 (tpp) REVERT: A 213 HIS cc_start: 0.7611 (p-80) cc_final: 0.7380 (p-80) REVERT: A 246 SER cc_start: 0.9155 (m) cc_final: 0.8853 (p) REVERT: A 274 PHE cc_start: 0.7962 (t80) cc_final: 0.7442 (t80) REVERT: A 283 LEU cc_start: 0.9469 (mt) cc_final: 0.8878 (tp) REVERT: A 287 TYR cc_start: 0.8295 (m-80) cc_final: 0.7472 (m-80) REVERT: A 303 ILE cc_start: 0.8900 (mt) cc_final: 0.8499 (mt) REVERT: A 306 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7898 (mm-40) REVERT: A 307 PHE cc_start: 0.8625 (m-80) cc_final: 0.8348 (m-80) REVERT: A 317 LYS cc_start: 0.7660 (ttmt) cc_final: 0.7290 (tppt) REVERT: A 320 TYR cc_start: 0.7626 (m-10) cc_final: 0.7236 (m-80) REVERT: A 334 PHE cc_start: 0.8802 (t80) cc_final: 0.8419 (t80) REVERT: A 337 ASP cc_start: 0.8301 (m-30) cc_final: 0.7927 (m-30) REVERT: A 346 ASN cc_start: 0.8176 (m-40) cc_final: 0.7902 (m-40) REVERT: B 23 LYS cc_start: 0.9093 (mtmt) cc_final: 0.8776 (mttm) REVERT: B 52 ARG cc_start: 0.8093 (mtp85) cc_final: 0.7750 (ptp90) REVERT: B 101 MET cc_start: 0.8036 (mmm) cc_final: 0.7743 (tpp) REVERT: B 102 THR cc_start: 0.8550 (t) cc_final: 0.8308 (m) REVERT: B 154 ASP cc_start: 0.8104 (t0) cc_final: 0.7495 (t0) REVERT: B 156 GLN cc_start: 0.6822 (mm-40) cc_final: 0.6525 (mp10) REVERT: B 289 TYR cc_start: 0.7009 (m-80) cc_final: 0.6205 (m-80) REVERT: B 298 ASP cc_start: 0.7666 (t0) cc_final: 0.7419 (t70) REVERT: Y 13 ARG cc_start: 0.8311 (ptp-170) cc_final: 0.8053 (ptp-170) REVERT: Y 21 MET cc_start: 0.8735 (tmm) cc_final: 0.7902 (tmm) REVERT: Y 22 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8245 (mm-30) REVERT: Y 32 LYS cc_start: 0.8335 (mmtt) cc_final: 0.7951 (mmtt) REVERT: N 110 PHE cc_start: 0.8779 (t80) cc_final: 0.8405 (t80) REVERT: N 179 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7484 (tm-30) REVERT: N 195 LEU cc_start: 0.9364 (mt) cc_final: 0.9074 (tp) REVERT: N 219 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8518 (tm) REVERT: N 220 GLU cc_start: 0.8520 (mm-30) cc_final: 0.7937 (mp0) REVERT: N 230 MET cc_start: 0.7365 (ttp) cc_final: 0.6922 (tmm) REVERT: C 197 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7763 (mm-30) REVERT: C 255 GLU cc_start: 0.8445 (tp30) cc_final: 0.8170 (tp30) REVERT: C 321 SER cc_start: 0.7366 (m) cc_final: 0.6924 (p) REVERT: C 327 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7752 (tm-30) REVERT: C 357 GLN cc_start: 0.8219 (tp40) cc_final: 0.7408 (tm-30) REVERT: C 375 PHE cc_start: 0.8608 (m-80) cc_final: 0.8238 (m-80) REVERT: C 379 TYR cc_start: 0.8096 (t80) cc_final: 0.7625 (t80) REVERT: C 399 ASN cc_start: 0.8155 (p0) cc_final: 0.7788 (p0) REVERT: C 415 MET cc_start: 0.7549 (ttm) cc_final: 0.7222 (ttm) REVERT: C 445 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7144 (mm-30) REVERT: C 449 LYS cc_start: 0.8977 (mtmt) cc_final: 0.8727 (ttmm) REVERT: C 454 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8616 (mm) REVERT: C 457 HIS cc_start: 0.7809 (OUTLIER) cc_final: 0.7412 (t-90) REVERT: C 472 ASP cc_start: 0.7869 (m-30) cc_final: 0.7531 (m-30) REVERT: C 548 LYS cc_start: 0.8477 (mmmt) cc_final: 0.8177 (mmmt) REVERT: C 559 ASP cc_start: 0.7615 (t0) cc_final: 0.7200 (t0) REVERT: C 567 LYS cc_start: 0.8410 (ttpp) cc_final: 0.7982 (ttpp) REVERT: C 568 TRP cc_start: 0.8000 (m100) cc_final: 0.7352 (m100) REVERT: C 626 GLN cc_start: 0.7409 (mp10) cc_final: 0.7072 (mp10) REVERT: C 708 TRP cc_start: 0.6950 (p-90) cc_final: 0.6424 (m100) REVERT: C 743 LYS cc_start: 0.8299 (tmtt) cc_final: 0.8052 (tmtt) REVERT: C 795 SER cc_start: 0.8861 (m) cc_final: 0.8424 (p) REVERT: C 812 VAL cc_start: 0.8574 (t) cc_final: 0.8308 (p) REVERT: D 62 MET cc_start: 0.7971 (ptm) cc_final: 0.7767 (ttp) REVERT: D 95 ARG cc_start: 0.7852 (tpp80) cc_final: 0.7461 (mmm-85) REVERT: D 107 GLU cc_start: 0.7293 (mp0) cc_final: 0.6122 (mp0) REVERT: D 112 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7718 (mtpt) REVERT: D 222 GLU cc_start: 0.7991 (mp0) cc_final: 0.7777 (mp0) REVERT: D 272 MET cc_start: 0.7922 (ttt) cc_final: 0.7578 (mtt) REVERT: D 311 MET cc_start: 0.7745 (ptp) cc_final: 0.7419 (ptp) REVERT: D 319 PHE cc_start: 0.7680 (p90) cc_final: 0.7405 (p90) REVERT: D 353 LYS cc_start: 0.8970 (mmtm) cc_final: 0.8678 (mmmm) REVERT: D 397 ARG cc_start: 0.7934 (mmm160) cc_final: 0.7096 (mmm160) REVERT: D 432 GLN cc_start: 0.8745 (mt0) cc_final: 0.8354 (mm-40) REVERT: D 528 MET cc_start: 0.6952 (mmp) cc_final: 0.6498 (mmp) REVERT: D 626 GLU cc_start: 0.7659 (pt0) cc_final: 0.7171 (pp20) REVERT: D 678 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.8077 (t) REVERT: D 688 ASP cc_start: 0.8162 (m-30) cc_final: 0.7871 (p0) outliers start: 75 outliers final: 53 residues processed: 558 average time/residue: 0.3728 time to fit residues: 295.1159 Evaluate side-chains 552 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 494 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 502 ASN Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 615 TYR Chi-restraints excluded: chain C residue 645 PHE Chi-restraints excluded: chain C residue 663 CYS Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 553 CYS Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 608 ASP Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain D residue 741 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 0.0020 chunk 25 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 188 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 222 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 269 ASN B 44 GLN B 156 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18896 Z= 0.189 Angle : 0.760 26.450 25600 Z= 0.362 Chirality : 0.056 1.905 2874 Planarity : 0.004 0.049 3237 Dihedral : 4.852 77.207 2548 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.80 % Rotamer: Outliers : 3.18 % Allowed : 21.26 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2315 helix: 0.76 (0.17), residues: 955 sheet: 0.27 (0.24), residues: 467 loop : -0.80 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 562 HIS 0.004 0.001 HIS D 355 PHE 0.027 0.002 PHE D 740 TYR 0.030 0.001 TYR D 342 ARG 0.011 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 519 time to evaluate : 2.137 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 9 ASP cc_start: 0.8598 (m-30) cc_final: 0.8148 (m-30) REVERT: A 10 LYS cc_start: 0.8924 (mttt) cc_final: 0.8433 (mtmm) REVERT: A 26 ASP cc_start: 0.7796 (m-30) cc_final: 0.7525 (p0) REVERT: A 29 LYS cc_start: 0.8617 (tmtt) cc_final: 0.8235 (tmtt) REVERT: A 32 ARG cc_start: 0.7448 (mpt-90) cc_final: 0.7059 (mpt-90) REVERT: A 129 ARG cc_start: 0.7453 (tpm170) cc_final: 0.7173 (tpm170) REVERT: A 154 TYR cc_start: 0.7912 (m-80) cc_final: 0.7482 (m-80) REVERT: A 158 ASP cc_start: 0.7508 (t0) cc_final: 0.7184 (t0) REVERT: A 189 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.6411 (t80) REVERT: A 194 LEU cc_start: 0.8335 (mp) cc_final: 0.7691 (tp) REVERT: A 240 MET cc_start: 0.8070 (tmm) cc_final: 0.7839 (ppp) REVERT: A 246 SER cc_start: 0.9160 (m) cc_final: 0.8863 (p) REVERT: A 274 PHE cc_start: 0.7863 (t80) cc_final: 0.7354 (t80) REVERT: A 283 LEU cc_start: 0.9462 (mt) cc_final: 0.8762 (pp) REVERT: A 287 TYR cc_start: 0.8255 (m-80) cc_final: 0.7721 (m-80) REVERT: A 303 ILE cc_start: 0.8791 (mt) cc_final: 0.8583 (mm) REVERT: A 306 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7789 (mm-40) REVERT: A 323 PHE cc_start: 0.8131 (m-10) cc_final: 0.7863 (m-10) REVERT: A 334 PHE cc_start: 0.8762 (t80) cc_final: 0.8360 (t80) REVERT: A 337 ASP cc_start: 0.8267 (m-30) cc_final: 0.7982 (m-30) REVERT: A 341 ASP cc_start: 0.8320 (m-30) cc_final: 0.8028 (p0) REVERT: A 345 LYS cc_start: 0.8779 (ptpp) cc_final: 0.8567 (ptpp) REVERT: A 346 ASN cc_start: 0.8160 (m-40) cc_final: 0.7892 (m-40) REVERT: B 13 GLN cc_start: 0.8749 (tm-30) cc_final: 0.7960 (tm-30) REVERT: B 19 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8201 (mtm-85) REVERT: B 23 LYS cc_start: 0.9076 (mtmt) cc_final: 0.8788 (mttt) REVERT: B 52 ARG cc_start: 0.8032 (mtp85) cc_final: 0.7728 (ptp90) REVERT: B 101 MET cc_start: 0.7983 (mmm) cc_final: 0.7675 (tpp) REVERT: B 102 THR cc_start: 0.8550 (t) cc_final: 0.8294 (m) REVERT: B 129 ARG cc_start: 0.7933 (ptm160) cc_final: 0.7563 (ptm-80) REVERT: B 154 ASP cc_start: 0.8090 (t0) cc_final: 0.7759 (t0) REVERT: B 209 LYS cc_start: 0.8508 (mmtp) cc_final: 0.8023 (mmtm) REVERT: B 289 TYR cc_start: 0.6959 (m-80) cc_final: 0.6146 (m-80) REVERT: B 298 ASP cc_start: 0.7631 (t0) cc_final: 0.7375 (t70) REVERT: Y 13 ARG cc_start: 0.8314 (ptp-170) cc_final: 0.8053 (ptp-170) REVERT: Y 18 GLN cc_start: 0.8533 (tm-30) cc_final: 0.7902 (pp30) REVERT: Y 21 MET cc_start: 0.8624 (tmm) cc_final: 0.7912 (tmm) REVERT: Y 22 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8287 (mm-30) REVERT: Y 32 LYS cc_start: 0.8285 (mmtt) cc_final: 0.7936 (mmtt) REVERT: N 110 PHE cc_start: 0.8796 (t80) cc_final: 0.8470 (t80) REVERT: N 179 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7485 (tm-30) REVERT: N 195 LEU cc_start: 0.9353 (mt) cc_final: 0.9068 (tp) REVERT: N 219 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8454 (tp) REVERT: N 220 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8052 (mp0) REVERT: C 193 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8166 (mm-30) REVERT: C 197 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7736 (mm-30) REVERT: C 255 GLU cc_start: 0.8388 (tp30) cc_final: 0.8131 (tp30) REVERT: C 321 SER cc_start: 0.7326 (m) cc_final: 0.6894 (p) REVERT: C 327 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7783 (tm-30) REVERT: C 357 GLN cc_start: 0.8202 (tp40) cc_final: 0.7443 (tm-30) REVERT: C 375 PHE cc_start: 0.8584 (m-80) cc_final: 0.8170 (m-80) REVERT: C 399 ASN cc_start: 0.8172 (p0) cc_final: 0.7848 (p0) REVERT: C 415 MET cc_start: 0.7554 (ttm) cc_final: 0.7207 (ttm) REVERT: C 445 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7095 (mm-30) REVERT: C 449 LYS cc_start: 0.8980 (mtmt) cc_final: 0.8729 (ttmm) REVERT: C 454 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8569 (mm) REVERT: C 457 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.7352 (t-90) REVERT: C 459 GLU cc_start: 0.8518 (mp0) cc_final: 0.7933 (mp0) REVERT: C 472 ASP cc_start: 0.7928 (m-30) cc_final: 0.7614 (m-30) REVERT: C 548 LYS cc_start: 0.8462 (mmmt) cc_final: 0.8194 (mmmt) REVERT: C 567 LYS cc_start: 0.8394 (ttpp) cc_final: 0.8011 (ttpp) REVERT: C 598 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8691 (tp) REVERT: C 626 GLN cc_start: 0.7360 (mp10) cc_final: 0.7078 (mp10) REVERT: C 708 TRP cc_start: 0.6900 (p-90) cc_final: 0.6382 (m100) REVERT: C 743 LYS cc_start: 0.8342 (tmtt) cc_final: 0.8113 (tmtt) REVERT: C 795 SER cc_start: 0.8859 (m) cc_final: 0.8442 (p) REVERT: C 812 VAL cc_start: 0.8498 (t) cc_final: 0.8239 (p) REVERT: D 95 ARG cc_start: 0.7893 (tpp80) cc_final: 0.7497 (mmm-85) REVERT: D 107 GLU cc_start: 0.7281 (mp0) cc_final: 0.5871 (mp0) REVERT: D 112 LYS cc_start: 0.8210 (mtpp) cc_final: 0.7832 (ttpt) REVERT: D 222 GLU cc_start: 0.7962 (mp0) cc_final: 0.7749 (mp0) REVERT: D 230 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6777 (mm-30) REVERT: D 272 MET cc_start: 0.7934 (ttt) cc_final: 0.7626 (mtt) REVERT: D 276 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8339 (ptmt) REVERT: D 311 MET cc_start: 0.7700 (ptp) cc_final: 0.7334 (ptp) REVERT: D 319 PHE cc_start: 0.7642 (p90) cc_final: 0.7351 (p90) REVERT: D 353 LYS cc_start: 0.8960 (mmtm) cc_final: 0.8718 (mmmt) REVERT: D 355 HIS cc_start: 0.7612 (p-80) cc_final: 0.7118 (p90) REVERT: D 397 ARG cc_start: 0.7887 (mmm160) cc_final: 0.7209 (mmm160) REVERT: D 432 GLN cc_start: 0.8726 (mt0) cc_final: 0.8426 (mm-40) REVERT: D 493 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6911 (mmm) REVERT: D 528 MET cc_start: 0.6907 (mmp) cc_final: 0.6610 (mmp) REVERT: D 626 GLU cc_start: 0.7555 (pt0) cc_final: 0.7092 (pp20) REVERT: D 646 GLU cc_start: 0.7184 (pm20) cc_final: 0.6964 (pm20) REVERT: D 678 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8091 (t) outliers start: 64 outliers final: 41 residues processed: 553 average time/residue: 0.3587 time to fit residues: 281.3209 Evaluate side-chains 547 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 499 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 456 ARG Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 645 PHE Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 824 MET Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 558 TRP Chi-restraints excluded: chain D residue 608 ASP Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 175 optimal weight: 0.0980 chunk 202 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 9 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 88 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 18 GLN ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 HIS ** D 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18896 Z= 0.207 Angle : 0.789 26.545 25600 Z= 0.379 Chirality : 0.057 1.881 2874 Planarity : 0.004 0.068 3237 Dihedral : 4.904 77.670 2548 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.67 % Rotamer: Outliers : 2.98 % Allowed : 22.01 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2315 helix: 0.77 (0.17), residues: 955 sheet: 0.29 (0.24), residues: 467 loop : -0.77 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 562 HIS 0.004 0.001 HIS D 355 PHE 0.048 0.002 PHE A 307 TYR 0.029 0.001 TYR D 342 ARG 0.016 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 515 time to evaluate : 1.956 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 9 ASP cc_start: 0.8610 (m-30) cc_final: 0.8154 (m-30) REVERT: A 10 LYS cc_start: 0.8927 (mttt) cc_final: 0.8399 (mtmm) REVERT: A 21 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7460 (ttp80) REVERT: A 29 LYS cc_start: 0.8641 (tmtt) cc_final: 0.8225 (tmtt) REVERT: A 32 ARG cc_start: 0.7480 (mpt-90) cc_final: 0.7127 (mpt-90) REVERT: A 129 ARG cc_start: 0.7346 (tpm170) cc_final: 0.7053 (tpm170) REVERT: A 154 TYR cc_start: 0.7932 (m-80) cc_final: 0.7491 (m-80) REVERT: A 158 ASP cc_start: 0.7541 (t0) cc_final: 0.7197 (t0) REVERT: A 189 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.6447 (t80) REVERT: A 194 LEU cc_start: 0.8012 (mp) cc_final: 0.7695 (tp) REVERT: A 232 LEU cc_start: 0.8451 (tt) cc_final: 0.8226 (pp) REVERT: A 240 MET cc_start: 0.8011 (tmm) cc_final: 0.7805 (ppp) REVERT: A 246 SER cc_start: 0.9140 (m) cc_final: 0.8817 (p) REVERT: A 274 PHE cc_start: 0.7885 (t80) cc_final: 0.7382 (t80) REVERT: A 283 LEU cc_start: 0.9471 (mt) cc_final: 0.8768 (pp) REVERT: A 287 TYR cc_start: 0.8258 (m-80) cc_final: 0.7674 (m-80) REVERT: A 334 PHE cc_start: 0.8763 (t80) cc_final: 0.8349 (t80) REVERT: A 337 ASP cc_start: 0.8296 (m-30) cc_final: 0.7996 (m-30) REVERT: A 341 ASP cc_start: 0.8312 (m-30) cc_final: 0.7904 (p0) REVERT: A 346 ASN cc_start: 0.8149 (m-40) cc_final: 0.7888 (m-40) REVERT: B 23 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8726 (mttm) REVERT: B 52 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7716 (ptp90) REVERT: B 101 MET cc_start: 0.7946 (mmm) cc_final: 0.7663 (tpp) REVERT: B 102 THR cc_start: 0.8557 (t) cc_final: 0.8296 (m) REVERT: B 129 ARG cc_start: 0.8019 (ptm160) cc_final: 0.7705 (ptm-80) REVERT: B 154 ASP cc_start: 0.8090 (t0) cc_final: 0.7699 (t0) REVERT: B 156 GLN cc_start: 0.6976 (mm-40) cc_final: 0.6719 (mp10) REVERT: B 209 LYS cc_start: 0.8541 (mmtp) cc_final: 0.8054 (mmtm) REVERT: B 226 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8372 (mm-30) REVERT: B 280 LYS cc_start: 0.7758 (tppt) cc_final: 0.7456 (tppp) REVERT: B 289 TYR cc_start: 0.7010 (m-80) cc_final: 0.6187 (m-80) REVERT: B 337 LYS cc_start: 0.8447 (mmmm) cc_final: 0.7925 (mmmm) REVERT: Y 18 GLN cc_start: 0.8574 (tm130) cc_final: 0.7935 (pp30) REVERT: Y 21 MET cc_start: 0.8531 (tmm) cc_final: 0.7761 (tmm) REVERT: Y 22 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8238 (mm-30) REVERT: Y 32 LYS cc_start: 0.8296 (mmtt) cc_final: 0.8015 (mmtt) REVERT: N 100 ILE cc_start: 0.8935 (tp) cc_final: 0.8696 (tt) REVERT: N 110 PHE cc_start: 0.8831 (t80) cc_final: 0.8500 (t80) REVERT: N 179 GLN cc_start: 0.7802 (tm-30) cc_final: 0.7483 (tm-30) REVERT: N 195 LEU cc_start: 0.9353 (mt) cc_final: 0.9084 (tp) REVERT: N 219 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8430 (tp) REVERT: N 230 MET cc_start: 0.7624 (tmm) cc_final: 0.7291 (tmm) REVERT: C 197 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7727 (mm-30) REVERT: C 321 SER cc_start: 0.7325 (m) cc_final: 0.6895 (p) REVERT: C 327 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7798 (tm-30) REVERT: C 357 GLN cc_start: 0.8178 (tp40) cc_final: 0.7449 (tm-30) REVERT: C 375 PHE cc_start: 0.8545 (m-80) cc_final: 0.8185 (m-80) REVERT: C 380 LYS cc_start: 0.8149 (mmmm) cc_final: 0.7801 (mmmm) REVERT: C 399 ASN cc_start: 0.8223 (p0) cc_final: 0.7629 (p0) REVERT: C 414 GLU cc_start: 0.6823 (pt0) cc_final: 0.6390 (pt0) REVERT: C 415 MET cc_start: 0.7393 (ttm) cc_final: 0.6949 (ttm) REVERT: C 428 VAL cc_start: 0.6628 (OUTLIER) cc_final: 0.6372 (p) REVERT: C 441 MET cc_start: 0.7900 (tpp) cc_final: 0.7037 (tpp) REVERT: C 445 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6816 (pt0) REVERT: C 449 LYS cc_start: 0.8992 (mtmt) cc_final: 0.8752 (ttmm) REVERT: C 454 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8548 (mm) REVERT: C 457 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.7404 (t-90) REVERT: C 459 GLU cc_start: 0.8498 (mp0) cc_final: 0.7904 (mp0) REVERT: C 472 ASP cc_start: 0.7964 (m-30) cc_final: 0.7628 (m-30) REVERT: C 483 LYS cc_start: 0.8650 (tmtt) cc_final: 0.8289 (mtmm) REVERT: C 513 MET cc_start: 0.7411 (mmt) cc_final: 0.7166 (mmt) REVERT: C 567 LYS cc_start: 0.8413 (ttpp) cc_final: 0.7981 (ttpp) REVERT: C 568 TRP cc_start: 0.7955 (m100) cc_final: 0.7285 (m100) REVERT: C 598 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8754 (tp) REVERT: C 626 GLN cc_start: 0.7462 (mp10) cc_final: 0.7188 (mp10) REVERT: C 708 TRP cc_start: 0.6895 (p-90) cc_final: 0.6410 (m100) REVERT: C 743 LYS cc_start: 0.8345 (tmtt) cc_final: 0.8110 (tmtt) REVERT: C 795 SER cc_start: 0.8848 (m) cc_final: 0.8408 (p) REVERT: C 812 VAL cc_start: 0.8498 (t) cc_final: 0.8230 (p) REVERT: D 95 ARG cc_start: 0.7882 (tpp80) cc_final: 0.7504 (mmm-85) REVERT: D 107 GLU cc_start: 0.7285 (mp0) cc_final: 0.6616 (mp0) REVERT: D 112 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7854 (mtpt) REVERT: D 222 GLU cc_start: 0.7970 (mp0) cc_final: 0.7748 (mp0) REVERT: D 230 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6818 (mm-30) REVERT: D 272 MET cc_start: 0.7960 (ttt) cc_final: 0.7628 (mtt) REVERT: D 276 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8359 (ptmt) REVERT: D 311 MET cc_start: 0.7715 (ptp) cc_final: 0.7353 (ptp) REVERT: D 324 SER cc_start: 0.9002 (m) cc_final: 0.8665 (t) REVERT: D 353 LYS cc_start: 0.8974 (mmtm) cc_final: 0.8755 (mmmt) REVERT: D 355 HIS cc_start: 0.7624 (p-80) cc_final: 0.7409 (p-80) REVERT: D 397 ARG cc_start: 0.7899 (mmm160) cc_final: 0.7060 (mmm160) REVERT: D 421 GLU cc_start: 0.6962 (tp30) cc_final: 0.6636 (tp30) REVERT: D 432 GLN cc_start: 0.8767 (mt0) cc_final: 0.8522 (mm-40) REVERT: D 528 MET cc_start: 0.6952 (mmp) cc_final: 0.6670 (mmp) REVERT: D 626 GLU cc_start: 0.7595 (pt0) cc_final: 0.7105 (pp20) REVERT: D 646 GLU cc_start: 0.7221 (pm20) cc_final: 0.7006 (pm20) REVERT: D 678 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8127 (t) REVERT: D 702 MET cc_start: 0.8550 (mmp) cc_final: 0.8204 (mmm) outliers start: 60 outliers final: 49 residues processed: 546 average time/residue: 0.3626 time to fit residues: 282.7543 Evaluate side-chains 554 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 498 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 615 TYR Chi-restraints excluded: chain C residue 645 PHE Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 824 MET Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 558 TRP Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 608 ASP Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 chunk 136 optimal weight: 0.0470 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 18896 Z= 0.270 Angle : 0.832 26.540 25600 Z= 0.401 Chirality : 0.057 1.865 2874 Planarity : 0.004 0.054 3237 Dihedral : 5.063 78.249 2548 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.63 % Favored : 96.33 % Rotamer: Outliers : 3.43 % Allowed : 21.71 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 2315 helix: 0.63 (0.17), residues: 949 sheet: 0.26 (0.24), residues: 472 loop : -0.76 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 562 HIS 0.006 0.001 HIS C 689 PHE 0.061 0.002 PHE A 307 TYR 0.028 0.002 TYR D 338 ARG 0.015 0.001 ARG D 418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 509 time to evaluate : 2.272 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: symmetry clash REVERT: A 9 ASP cc_start: 0.8626 (m-30) cc_final: 0.8171 (m-30) REVERT: A 10 LYS cc_start: 0.8951 (mttt) cc_final: 0.8427 (mtmm) REVERT: A 18 MET cc_start: 0.7736 (mmm) cc_final: 0.7403 (tpp) REVERT: A 21 ARG cc_start: 0.7753 (ttp80) cc_final: 0.7133 (ttp80) REVERT: A 25 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7727 (mt-10) REVERT: A 29 LYS cc_start: 0.8692 (tmtt) cc_final: 0.8288 (tmtt) REVERT: A 32 ARG cc_start: 0.7539 (mpt-90) cc_final: 0.7146 (mpt-90) REVERT: A 129 ARG cc_start: 0.7362 (tpm170) cc_final: 0.7095 (tpm170) REVERT: A 158 ASP cc_start: 0.7569 (t0) cc_final: 0.7300 (t0) REVERT: A 189 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.6444 (t80) REVERT: A 194 LEU cc_start: 0.8046 (mp) cc_final: 0.7724 (tp) REVERT: A 213 HIS cc_start: 0.7899 (p-80) cc_final: 0.7385 (p-80) REVERT: A 232 LEU cc_start: 0.8418 (tt) cc_final: 0.8203 (pp) REVERT: A 240 MET cc_start: 0.8133 (tmm) cc_final: 0.7893 (ppp) REVERT: A 246 SER cc_start: 0.9180 (m) cc_final: 0.8869 (p) REVERT: A 274 PHE cc_start: 0.7978 (t80) cc_final: 0.7503 (t80) REVERT: A 283 LEU cc_start: 0.9407 (mt) cc_final: 0.8864 (pt) REVERT: A 287 TYR cc_start: 0.8304 (m-80) cc_final: 0.7653 (m-80) REVERT: A 334 PHE cc_start: 0.8807 (t80) cc_final: 0.8383 (t80) REVERT: A 337 ASP cc_start: 0.8297 (m-30) cc_final: 0.7937 (m-30) REVERT: A 341 ASP cc_start: 0.8342 (m-30) cc_final: 0.7846 (p0) REVERT: A 345 LYS cc_start: 0.8800 (ptpp) cc_final: 0.8265 (pttm) REVERT: A 346 ASN cc_start: 0.8153 (m-40) cc_final: 0.7895 (m-40) REVERT: B 23 LYS cc_start: 0.9069 (mtmt) cc_final: 0.8717 (mttm) REVERT: B 52 ARG cc_start: 0.7998 (mtp85) cc_final: 0.7700 (ptp90) REVERT: B 96 ARG cc_start: 0.6387 (mmp80) cc_final: 0.6013 (mmp80) REVERT: B 101 MET cc_start: 0.7949 (mmm) cc_final: 0.7656 (tpp) REVERT: B 102 THR cc_start: 0.8585 (t) cc_final: 0.8314 (m) REVERT: B 154 ASP cc_start: 0.8070 (t0) cc_final: 0.7494 (t0) REVERT: B 156 GLN cc_start: 0.7008 (mm110) cc_final: 0.6699 (mp10) REVERT: B 209 LYS cc_start: 0.8567 (mmtp) cc_final: 0.8083 (mmtm) REVERT: B 226 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8383 (mm-30) REVERT: B 256 ARG cc_start: 0.8071 (mtm180) cc_final: 0.7626 (mtm180) REVERT: B 289 TYR cc_start: 0.7117 (m-80) cc_final: 0.6224 (m-80) REVERT: Y 18 GLN cc_start: 0.8597 (tm130) cc_final: 0.7857 (pp30) REVERT: Y 21 MET cc_start: 0.8582 (tmm) cc_final: 0.7826 (tmm) REVERT: Y 32 LYS cc_start: 0.8359 (mmtt) cc_final: 0.8035 (mmtt) REVERT: N 100 ILE cc_start: 0.8983 (tp) cc_final: 0.8761 (tt) REVERT: N 110 PHE cc_start: 0.8859 (t80) cc_final: 0.8531 (t80) REVERT: N 195 LEU cc_start: 0.9372 (mt) cc_final: 0.9102 (tp) REVERT: N 219 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8498 (tm) REVERT: N 230 MET cc_start: 0.7682 (tmm) cc_final: 0.7347 (tmm) REVERT: C 193 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8119 (mm-30) REVERT: C 197 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7738 (mm-30) REVERT: C 279 ARG cc_start: 0.7892 (ttm-80) cc_final: 0.7643 (mtp-110) REVERT: C 321 SER cc_start: 0.7377 (m) cc_final: 0.6938 (p) REVERT: C 327 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7734 (tm-30) REVERT: C 357 GLN cc_start: 0.8177 (tp40) cc_final: 0.7433 (tm-30) REVERT: C 375 PHE cc_start: 0.8604 (m-80) cc_final: 0.8179 (m-80) REVERT: C 380 LYS cc_start: 0.8083 (mmmm) cc_final: 0.7752 (mmmm) REVERT: C 399 ASN cc_start: 0.8325 (p0) cc_final: 0.7983 (p0) REVERT: C 415 MET cc_start: 0.7417 (ttm) cc_final: 0.6934 (ttm) REVERT: C 441 MET cc_start: 0.7926 (tpp) cc_final: 0.7144 (tpp) REVERT: C 445 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6856 (pt0) REVERT: C 449 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8793 (ttmm) REVERT: C 454 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8536 (mm) REVERT: C 457 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.7444 (t-90) REVERT: C 459 GLU cc_start: 0.8469 (mp0) cc_final: 0.7797 (mp0) REVERT: C 472 ASP cc_start: 0.7928 (m-30) cc_final: 0.7595 (m-30) REVERT: C 513 MET cc_start: 0.7341 (mmt) cc_final: 0.7009 (mmt) REVERT: C 540 GLU cc_start: 0.6956 (mp0) cc_final: 0.6569 (mp0) REVERT: C 567 LYS cc_start: 0.8484 (ttpp) cc_final: 0.8114 (ttpp) REVERT: C 568 TRP cc_start: 0.8002 (m100) cc_final: 0.7462 (m100) REVERT: C 598 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8783 (tp) REVERT: C 626 GLN cc_start: 0.7647 (mp10) cc_final: 0.7294 (mp10) REVERT: C 708 TRP cc_start: 0.6847 (p-90) cc_final: 0.6420 (m100) REVERT: C 743 LYS cc_start: 0.8353 (tmtt) cc_final: 0.8111 (tmtt) REVERT: C 795 SER cc_start: 0.8874 (m) cc_final: 0.8444 (p) REVERT: C 812 VAL cc_start: 0.8538 (t) cc_final: 0.8252 (p) REVERT: D 92 SER cc_start: 0.8771 (t) cc_final: 0.8238 (p) REVERT: D 95 ARG cc_start: 0.7949 (tpp80) cc_final: 0.7589 (mmm-85) REVERT: D 107 GLU cc_start: 0.7273 (mp0) cc_final: 0.6045 (mp0) REVERT: D 112 LYS cc_start: 0.8128 (mtpp) cc_final: 0.7749 (mtpt) REVERT: D 222 GLU cc_start: 0.8011 (mp0) cc_final: 0.7779 (mp0) REVERT: D 230 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6838 (mm-30) REVERT: D 276 LYS cc_start: 0.8720 (ttmt) cc_final: 0.8338 (ptmt) REVERT: D 290 TRP cc_start: 0.8791 (p90) cc_final: 0.8525 (p90) REVERT: D 311 MET cc_start: 0.7819 (ptp) cc_final: 0.7457 (ptp) REVERT: D 324 SER cc_start: 0.9005 (m) cc_final: 0.8687 (t) REVERT: D 353 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8759 (mmmt) REVERT: D 355 HIS cc_start: 0.7614 (p-80) cc_final: 0.7396 (p-80) REVERT: D 397 ARG cc_start: 0.7872 (mmm160) cc_final: 0.7206 (mmm160) REVERT: D 403 MET cc_start: 0.8569 (mmm) cc_final: 0.8314 (tpt) REVERT: D 418 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.7943 (ptp90) REVERT: D 421 GLU cc_start: 0.7012 (tp30) cc_final: 0.6791 (tp30) REVERT: D 432 GLN cc_start: 0.8753 (mt0) cc_final: 0.8511 (mm-40) REVERT: D 626 GLU cc_start: 0.7690 (pt0) cc_final: 0.7177 (pp20) REVERT: D 678 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8058 (p) REVERT: D 702 MET cc_start: 0.8573 (mmp) cc_final: 0.8260 (mmm) outliers start: 69 outliers final: 52 residues processed: 544 average time/residue: 0.3782 time to fit residues: 289.6144 Evaluate side-chains 555 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 497 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 615 TYR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 824 MET Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 558 TRP Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 608 ASP Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 0.0980 chunk 133 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 230 optimal weight: 0.7980 chunk 211 optimal weight: 0.0970 chunk 183 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18896 Z= 0.208 Angle : 0.840 26.538 25600 Z= 0.403 Chirality : 0.057 1.880 2874 Planarity : 0.004 0.051 3237 Dihedral : 4.975 78.361 2548 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.72 % Rotamer: Outliers : 2.78 % Allowed : 22.65 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 2315 helix: 0.64 (0.17), residues: 955 sheet: 0.21 (0.24), residues: 480 loop : -0.74 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A 258 HIS 0.003 0.001 HIS D 355 PHE 0.063 0.002 PHE A 307 TYR 0.027 0.001 TYR D 338 ARG 0.011 0.001 ARG D 418 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4630 Ramachandran restraints generated. 2315 Oldfield, 0 Emsley, 2315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 510 time to evaluate : 2.184 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 9 ASP cc_start: 0.8626 (m-30) cc_final: 0.8173 (m-30) REVERT: A 10 LYS cc_start: 0.8896 (mttt) cc_final: 0.8374 (mtmm) REVERT: A 21 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7577 (ttp80) REVERT: A 29 LYS cc_start: 0.8658 (tmtt) cc_final: 0.8300 (tmtt) REVERT: A 32 ARG cc_start: 0.7553 (mpt-90) cc_final: 0.7190 (mpt-90) REVERT: A 129 ARG cc_start: 0.7468 (tpm170) cc_final: 0.7181 (tpm170) REVERT: A 158 ASP cc_start: 0.7570 (t0) cc_final: 0.7293 (t0) REVERT: A 189 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6363 (t80) REVERT: A 192 LYS cc_start: 0.8996 (ptpp) cc_final: 0.8791 (ptpp) REVERT: A 194 LEU cc_start: 0.8010 (mp) cc_final: 0.7648 (tp) REVERT: A 213 HIS cc_start: 0.7762 (p-80) cc_final: 0.7301 (p-80) REVERT: A 246 SER cc_start: 0.9156 (m) cc_final: 0.8843 (p) REVERT: A 277 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8071 (ptpp) REVERT: A 283 LEU cc_start: 0.9361 (mt) cc_final: 0.8782 (pt) REVERT: A 287 TYR cc_start: 0.8233 (m-80) cc_final: 0.7581 (m-80) REVERT: A 298 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7956 (tt0) REVERT: A 318 GLU cc_start: 0.7698 (pm20) cc_final: 0.7160 (pm20) REVERT: A 334 PHE cc_start: 0.8763 (t80) cc_final: 0.8409 (t80) REVERT: A 337 ASP cc_start: 0.8268 (m-30) cc_final: 0.8014 (m-30) REVERT: A 341 ASP cc_start: 0.8301 (m-30) cc_final: 0.7894 (p0) REVERT: B 23 LYS cc_start: 0.9045 (mtmt) cc_final: 0.8722 (mttt) REVERT: B 45 MET cc_start: 0.7893 (mmm) cc_final: 0.7618 (mmm) REVERT: B 52 ARG cc_start: 0.7967 (mtp85) cc_final: 0.7701 (ptp90) REVERT: B 61 MET cc_start: 0.8204 (tmm) cc_final: 0.7802 (ppp) REVERT: B 96 ARG cc_start: 0.6459 (mmp80) cc_final: 0.6069 (mmp80) REVERT: B 102 THR cc_start: 0.8578 (t) cc_final: 0.8308 (m) REVERT: B 129 ARG cc_start: 0.8090 (ptm160) cc_final: 0.7753 (ptm-80) REVERT: B 209 LYS cc_start: 0.8551 (mmtp) cc_final: 0.8090 (mmtm) REVERT: B 226 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8373 (mm-30) REVERT: B 256 ARG cc_start: 0.8043 (mtm180) cc_final: 0.7578 (mtm180) REVERT: B 289 TYR cc_start: 0.7021 (m-80) cc_final: 0.6133 (m-80) REVERT: B 337 LYS cc_start: 0.8430 (mmmm) cc_final: 0.7898 (mmmm) REVERT: Y 32 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7947 (mmtt) REVERT: N 100 ILE cc_start: 0.8923 (tp) cc_final: 0.8714 (tt) REVERT: N 110 PHE cc_start: 0.8858 (t80) cc_final: 0.8565 (t80) REVERT: N 179 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7536 (tm-30) REVERT: N 195 LEU cc_start: 0.9359 (mt) cc_final: 0.9089 (tp) REVERT: N 219 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8461 (tm) REVERT: N 220 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8107 (mp0) REVERT: N 230 MET cc_start: 0.7616 (tmm) cc_final: 0.7237 (tmm) REVERT: C 197 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7722 (mm-30) REVERT: C 255 GLU cc_start: 0.8366 (tp30) cc_final: 0.7929 (tp30) REVERT: C 321 SER cc_start: 0.7358 (m) cc_final: 0.6930 (p) REVERT: C 327 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7761 (tm-30) REVERT: C 357 GLN cc_start: 0.8133 (tp40) cc_final: 0.7430 (tm-30) REVERT: C 375 PHE cc_start: 0.8598 (m-80) cc_final: 0.8352 (m-80) REVERT: C 377 GLU cc_start: 0.6239 (tt0) cc_final: 0.6016 (tt0) REVERT: C 399 ASN cc_start: 0.8332 (p0) cc_final: 0.7791 (p0) REVERT: C 414 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6509 (pt0) REVERT: C 415 MET cc_start: 0.7427 (ttm) cc_final: 0.7010 (tpt) REVERT: C 444 GLN cc_start: 0.8444 (mp10) cc_final: 0.8116 (pm20) REVERT: C 449 LYS cc_start: 0.9003 (mtmt) cc_final: 0.8780 (ttmm) REVERT: C 454 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8505 (mm) REVERT: C 457 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7398 (t-90) REVERT: C 459 GLU cc_start: 0.8457 (mp0) cc_final: 0.7761 (mp0) REVERT: C 472 ASP cc_start: 0.7976 (m-30) cc_final: 0.7647 (m-30) REVERT: C 567 LYS cc_start: 0.8435 (ttpp) cc_final: 0.8059 (ttpp) REVERT: C 568 TRP cc_start: 0.7956 (m100) cc_final: 0.7342 (m100) REVERT: C 598 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8768 (tp) REVERT: C 626 GLN cc_start: 0.7511 (mp10) cc_final: 0.7284 (mp10) REVERT: C 708 TRP cc_start: 0.6828 (p-90) cc_final: 0.6435 (m100) REVERT: C 743 LYS cc_start: 0.8377 (tmtt) cc_final: 0.8176 (tmtt) REVERT: C 795 SER cc_start: 0.8843 (m) cc_final: 0.8424 (p) REVERT: C 812 VAL cc_start: 0.8502 (t) cc_final: 0.8223 (p) REVERT: D 92 SER cc_start: 0.8724 (t) cc_final: 0.8201 (p) REVERT: D 95 ARG cc_start: 0.7919 (tpp80) cc_final: 0.7549 (mmm-85) REVERT: D 107 GLU cc_start: 0.7247 (mp0) cc_final: 0.5673 (mp0) REVERT: D 112 LYS cc_start: 0.8184 (mtpp) cc_final: 0.7853 (ttpt) REVERT: D 222 GLU cc_start: 0.7977 (mp0) cc_final: 0.7747 (mp0) REVERT: D 230 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6817 (mm-30) REVERT: D 276 LYS cc_start: 0.8805 (ttmt) cc_final: 0.8515 (ptmt) REVERT: D 290 TRP cc_start: 0.8740 (p90) cc_final: 0.8482 (p90) REVERT: D 311 MET cc_start: 0.7769 (ptp) cc_final: 0.7392 (ptp) REVERT: D 324 SER cc_start: 0.9009 (m) cc_final: 0.8688 (t) REVERT: D 355 HIS cc_start: 0.7564 (p-80) cc_final: 0.7321 (p-80) REVERT: D 397 ARG cc_start: 0.7883 (mmm160) cc_final: 0.7281 (mmm160) REVERT: D 403 MET cc_start: 0.8494 (mmm) cc_final: 0.8213 (tpt) REVERT: D 418 ARG cc_start: 0.8193 (ttp-110) cc_final: 0.7965 (ptp90) REVERT: D 432 GLN cc_start: 0.8782 (mt0) cc_final: 0.8575 (mm-40) REVERT: D 528 MET cc_start: 0.6987 (mmp) cc_final: 0.6503 (mmm) REVERT: D 626 GLU cc_start: 0.7593 (pt0) cc_final: 0.7093 (pp20) REVERT: D 646 GLU cc_start: 0.7165 (pm20) cc_final: 0.6948 (pm20) REVERT: D 678 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.8047 (p) REVERT: D 702 MET cc_start: 0.8566 (mmp) cc_final: 0.8265 (mmm) outliers start: 56 outliers final: 46 residues processed: 537 average time/residue: 0.3563 time to fit residues: 272.6790 Evaluate side-chains 549 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 496 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 189 PHE Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 615 TYR Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 824 MET Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 558 TRP Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 608 ASP Chi-restraints excluded: chain D residue 629 SER Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 711 PHE Chi-restraints excluded: chain D residue 726 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 5.9990 chunk 56 optimal weight: 0.0670 chunk 168 optimal weight: 0.0470 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.118725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.099645 restraints weight = 43392.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.103411 restraints weight = 20866.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.105772 restraints weight = 11948.158| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.6305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18896 Z= 0.214 Angle : 0.848 26.562 25600 Z= 0.405 Chirality : 0.057 1.875 2874 Planarity : 0.004 0.047 3237 Dihedral : 4.966 78.381 2548 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 2.73 % Allowed : 23.10 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2315 helix: 0.68 (0.17), residues: 958 sheet: 0.23 (0.24), residues: 481 loop : -0.73 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 258 HIS 0.003 0.001 HIS D 355 PHE 0.062 0.002 PHE A 307 TYR 0.027 0.001 TYR D 338 ARG 0.011 0.001 ARG B 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5775.39 seconds wall clock time: 104 minutes 3.69 seconds (6243.69 seconds total)