Starting phenix.real_space_refine on Fri Feb 23 08:53:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo5_23461/02_2024/7lo5_23461_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo5_23461/02_2024/7lo5_23461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo5_23461/02_2024/7lo5_23461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo5_23461/02_2024/7lo5_23461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo5_23461/02_2024/7lo5_23461_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo5_23461/02_2024/7lo5_23461_updated.pdb" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 108 atoms to isotropic. 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 Ca 4 9.91 5 P 215 5.49 5 S 82 5.16 5 C 23071 2.51 5 N 6614 2.21 5 O 7463 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A GLU 603": "OE1" <-> "OE2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A ARG 674": "NH1" <-> "NH2" Residue "A GLU 676": "OE1" <-> "OE2" Residue "A TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A GLU 806": "OE1" <-> "OE2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A GLU 863": "OE1" <-> "OE2" Residue "A GLU 872": "OE1" <-> "OE2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 890": "NH1" <-> "NH2" Residue "A GLU 975": "OE1" <-> "OE2" Residue "A ARG 988": "NH1" <-> "NH2" Residue "A GLU 989": "OE1" <-> "OE2" Residue "A GLU 1001": "OE1" <-> "OE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B ASP 128": "OD1" <-> "OD2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B GLU 277": "OE1" <-> "OE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B ARG 395": "NH1" <-> "NH2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B GLU 603": "OE1" <-> "OE2" Residue "B GLU 614": "OE1" <-> "OE2" Residue "B GLU 641": "OE1" <-> "OE2" Residue "B GLU 659": "OE1" <-> "OE2" Residue "B ARG 696": "NH1" <-> "NH2" Residue "B GLU 699": "OE1" <-> "OE2" Residue "B GLU 736": "OE1" <-> "OE2" Residue "B ARG 845": "NH1" <-> "NH2" Residue "B GLU 846": "OE1" <-> "OE2" Residue "B GLU 872": "OE1" <-> "OE2" Residue "B ARG 890": "NH1" <-> "NH2" Residue "B TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 912": "OE1" <-> "OE2" Residue "B GLU 971": "OE1" <-> "OE2" Residue "B GLU 979": "OE1" <-> "OE2" Residue "B ARG 988": "NH1" <-> "NH2" Residue "C GLU 25": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C ASP 82": "OD1" <-> "OD2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C GLU 367": "OE1" <-> "OE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C ARG 400": "NH1" <-> "NH2" Residue "C ARG 440": "NH1" <-> "NH2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C GLU 469": "OE1" <-> "OE2" Residue "C GLU 506": "OE1" <-> "OE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C GLU 606": "OE1" <-> "OE2" Residue "C PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 659": "OE1" <-> "OE2" Residue "C ARG 696": "NH1" <-> "NH2" Residue "C GLU 806": "OE1" <-> "OE2" Residue "C GLU 821": "OE1" <-> "OE2" Residue "C ARG 845": "NH1" <-> "NH2" Residue "C ARG 870": "NH1" <-> "NH2" Residue "C ARG 875": "NH1" <-> "NH2" Residue "C GLU 881": "OE1" <-> "OE2" Residue "C ARG 884": "NH1" <-> "NH2" Residue "C ARG 890": "NH1" <-> "NH2" Residue "C GLU 920": "OE1" <-> "OE2" Residue "C ARG 929": "NH1" <-> "NH2" Residue "C GLU 971": "OE1" <-> "OE2" Residue "C ARG 988": "NH1" <-> "NH2" Residue "C GLU 1001": "OE1" <-> "OE2" Residue "D GLU 50": "OE1" <-> "OE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D ASP 82": "OD1" <-> "OD2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D GLU 149": "OE1" <-> "OE2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D GLU 299": "OE1" <-> "OE2" Residue "D GLU 350": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D ARG 395": "NH1" <-> "NH2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D ARG 436": "NH1" <-> "NH2" Residue "D ARG 440": "NH1" <-> "NH2" Residue "D GLU 458": "OE1" <-> "OE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 557": "OE1" <-> "OE2" Residue "D ARG 577": "NH1" <-> "NH2" Residue "D ARG 600": "NH1" <-> "NH2" Residue "D ARG 602": "NH1" <-> "NH2" Residue "D GLU 603": "OE1" <-> "OE2" Residue "D GLU 617": "OE1" <-> "OE2" Residue "D ASP 638": "OD1" <-> "OD2" Residue "D ASP 649": "OD1" <-> "OD2" Residue "D GLU 659": "OE1" <-> "OE2" Residue "D ARG 674": "NH1" <-> "NH2" Residue "D ASP 684": "OD1" <-> "OD2" Residue "D ARG 696": "NH1" <-> "NH2" Residue "D TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 714": "OE1" <-> "OE2" Residue "D ASP 716": "OD1" <-> "OD2" Residue "D GLU 806": "OE1" <-> "OE2" Residue "D ARG 822": "NH1" <-> "NH2" Residue "D GLU 846": "OE1" <-> "OE2" Residue "D ARG 862": "NH1" <-> "NH2" Residue "D GLU 863": "OE1" <-> "OE2" Residue "D ARG 875": "NH1" <-> "NH2" Residue "D GLU 881": "OE1" <-> "OE2" Residue "D ARG 890": "NH1" <-> "NH2" Residue "D GLU 920": "OE1" <-> "OE2" Residue "D ARG 929": "NH1" <-> "NH2" Residue "D ASP 935": "OD1" <-> "OD2" Residue "D GLU 1001": "OE1" <-> "OE2" Residue "D ARG 1002": "NH1" <-> "NH2" Residue "D GLU 1023": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37449 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 8249 Classifications: {'peptide': 1016} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 974} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 8230 Classifications: {'peptide': 1013} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 971} Chain breaks: 2 Chain: "C" Number of atoms: 8234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 8234 Classifications: {'peptide': 1014} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 972} Chain breaks: 2 Chain: "D" Number of atoms: 8221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8221 Classifications: {'peptide': 1012} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 970} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "F" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "G" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "I" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 561 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "K" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 504 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "L" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 521 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Time building chain proxies: 21.73, per 1000 atoms: 0.58 Number of scatterers: 37449 At special positions: 0 Unit cell: (113.025, 193.17, 221.94, 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) Ca 4 19.99 S 82 16.00 P 215 15.00 O 7463 8.00 N 6614 7.00 C 23071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.69 Conformation dependent library (CDL) restraints added in 6.0 seconds 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 173 helices and 31 sheets defined 46.0% alpha, 10.1% beta 87 base pairs and 180 stacking pairs defined. Time for finding SS restraints: 20.30 Creating SS restraints... Processing helix chain 'A' and resid 3 through 19 removed outlier: 3.519A pdb=" N ASP A 15 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 43 removed outlier: 5.247A pdb=" N ALA A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 97 Processing helix chain 'A' and resid 129 through 141 removed outlier: 3.560A pdb=" N ALA A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 174 removed outlier: 3.697A pdb=" N ASP A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Proline residue: A 162 - end of helix removed outlier: 3.706A pdb=" N ILE A 167 " --> pdb=" O HIS A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 202 through 221 removed outlier: 4.765A pdb=" N THR A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.664A pdb=" N GLU A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 242 removed outlier: 3.619A pdb=" N GLN A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 271 removed outlier: 5.042A pdb=" N ARG A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TYR A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE A 265 " --> pdb=" O TYR A 261 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 292 removed outlier: 4.509A pdb=" N ARG A 280 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 301 removed outlier: 3.668A pdb=" N GLU A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 326 Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 357 through 366 removed outlier: 4.332A pdb=" N GLU A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLN A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 393 Processing helix chain 'A' and resid 428 through 439 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 468 through 476 Processing helix chain 'A' and resid 478 through 481 No H-bonds generated for 'chain 'A' and resid 478 through 481' Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 522 through 534 removed outlier: 4.217A pdb=" N GLY A 526 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 527 " --> pdb=" O PHE A 524 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL A 531 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 532 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 557 Processing helix chain 'A' and resid 601 through 610 Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 647 through 650 No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'A' and resid 675 through 678 No H-bonds generated for 'chain 'A' and resid 675 through 678' Processing helix chain 'A' and resid 683 through 700 Processing helix chain 'A' and resid 705 through 709 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 766 through 769 No H-bonds generated for 'chain 'A' and resid 766 through 769' Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 845 through 857 Processing helix chain 'A' and resid 859 through 864 Processing helix chain 'A' and resid 866 through 871 removed outlier: 3.719A pdb=" N GLN A 871 " --> pdb=" O LEU A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 897 Processing helix chain 'A' and resid 919 through 925 Processing helix chain 'A' and resid 957 through 961 Processing helix chain 'A' and resid 969 through 977 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 996 through 1023 removed outlier: 5.000A pdb=" N GLU A1001 " --> pdb=" O ALA A 997 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARG A1002 " --> pdb=" O ASP A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 19 Processing helix chain 'B' and resid 25 through 42 removed outlier: 4.808A pdb=" N ALA B 30 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ALA B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE B 32 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 97 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 129 through 141 Processing helix chain 'B' and resid 145 through 177 removed outlier: 3.897A pdb=" N ASP B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Proline residue: B 162 - end of helix removed outlier: 3.727A pdb=" N ILE B 167 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLN B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.787A pdb=" N GLU B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 221 Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.572A pdb=" N HIS B 229 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 244 removed outlier: 3.614A pdb=" N GLN B 240 " --> pdb=" O GLN B 236 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU B 241 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR B 244 " --> pdb=" O GLN B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 271 removed outlier: 4.633A pdb=" N ARG B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE B 265 " --> pdb=" O TYR B 261 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 removed outlier: 5.179A pdb=" N ARG B 280 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 301 Processing helix chain 'B' and resid 308 through 325 Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'B' and resid 357 through 366 removed outlier: 4.200A pdb=" N GLU B 361 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLN B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 393 Processing helix chain 'B' and resid 428 through 437 Processing helix chain 'B' and resid 458 through 460 No H-bonds generated for 'chain 'B' and resid 458 through 460' Processing helix chain 'B' and resid 468 through 476 Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 492 through 503 Processing helix chain 'B' and resid 522 through 525 removed outlier: 3.970A pdb=" N ASP B 525 " --> pdb=" O ARG B 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 522 through 525' Processing helix chain 'B' and resid 527 through 534 removed outlier: 4.744A pdb=" N VAL B 532 " --> pdb=" O ARG B 528 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 Processing helix chain 'B' and resid 601 through 610 Processing helix chain 'B' and resid 647 through 651 Processing helix chain 'B' and resid 675 through 678 No H-bonds generated for 'chain 'B' and resid 675 through 678' Processing helix chain 'B' and resid 683 through 702 removed outlier: 4.198A pdb=" N LYS B 702 " --> pdb=" O ASN B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 709 Processing helix chain 'B' and resid 721 through 728 Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 766 through 768 No H-bonds generated for 'chain 'B' and resid 766 through 768' Processing helix chain 'B' and resid 828 through 837 Processing helix chain 'B' and resid 845 through 857 removed outlier: 5.034A pdb=" N HIS B 850 " --> pdb=" O GLU B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 864 Processing helix chain 'B' and resid 866 through 871 Processing helix chain 'B' and resid 883 through 897 Processing helix chain 'B' and resid 919 through 925 Processing helix chain 'B' and resid 958 through 960 No H-bonds generated for 'chain 'B' and resid 958 through 960' Processing helix chain 'B' and resid 969 through 977 removed outlier: 4.019A pdb=" N HIS B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 990 Processing helix chain 'B' and resid 996 through 1023 removed outlier: 5.095A pdb=" N GLU B1001 " --> pdb=" O ALA B 997 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG B1002 " --> pdb=" O ASP B 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 19 Processing helix chain 'C' and resid 25 through 43 removed outlier: 5.397A pdb=" N ALA C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE C 32 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY C 42 " --> pdb=" O ASP C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 97 removed outlier: 3.510A pdb=" N GLN C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 93 " --> pdb=" O ASP C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 141 Processing helix chain 'C' and resid 145 through 159 removed outlier: 3.687A pdb=" N ASP C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 173 removed outlier: 3.751A pdb=" N ILE C 167 " --> pdb=" O HIS C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 195 removed outlier: 3.597A pdb=" N GLU C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 221 Processing helix chain 'C' and resid 226 through 231 removed outlier: 4.033A pdb=" N GLU C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 243 removed outlier: 3.542A pdb=" N LEU C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 258 Processing helix chain 'C' and resid 261 through 270 removed outlier: 4.598A pdb=" N ILE C 265 " --> pdb=" O TYR C 261 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 270 " --> pdb=" O GLN C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 291 removed outlier: 4.963A pdb=" N ARG C 280 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU C 282 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG C 291 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 308 through 325 Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.852A pdb=" N LEU C 351 " --> pdb=" O PHE C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 366 Processing helix chain 'C' and resid 375 through 393 Processing helix chain 'C' and resid 407 through 410 No H-bonds generated for 'chain 'C' and resid 407 through 410' Processing helix chain 'C' and resid 428 through 439 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 468 through 481 removed outlier: 4.135A pdb=" N VAL C 479 " --> pdb=" O LYS C 475 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA C 480 " --> pdb=" O ALA C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 503 Processing helix chain 'C' and resid 516 through 520 Processing helix chain 'C' and resid 523 through 534 removed outlier: 4.255A pdb=" N GLY C 526 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL C 531 " --> pdb=" O ARG C 528 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL C 532 " --> pdb=" O LYS C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 557 Processing helix chain 'C' and resid 601 through 610 Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 647 through 651 Processing helix chain 'C' and resid 675 through 678 No H-bonds generated for 'chain 'C' and resid 675 through 678' Processing helix chain 'C' and resid 684 through 701 Processing helix chain 'C' and resid 705 through 709 Processing helix chain 'C' and resid 721 through 729 Processing helix chain 'C' and resid 766 through 769 No H-bonds generated for 'chain 'C' and resid 766 through 769' Processing helix chain 'C' and resid 771 through 773 No H-bonds generated for 'chain 'C' and resid 771 through 773' Processing helix chain 'C' and resid 828 through 837 Processing helix chain 'C' and resid 845 through 856 removed outlier: 3.534A pdb=" N ALA C 854 " --> pdb=" O HIS C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 864 Processing helix chain 'C' and resid 866 through 869 No H-bonds generated for 'chain 'C' and resid 866 through 869' Processing helix chain 'C' and resid 882 through 897 Processing helix chain 'C' and resid 919 through 924 Processing helix chain 'C' and resid 957 through 961 Processing helix chain 'C' and resid 969 through 976 Processing helix chain 'C' and resid 985 through 990 Processing helix chain 'C' and resid 996 through 1022 removed outlier: 4.962A pdb=" N GLU C1001 " --> pdb=" O ALA C 997 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ARG C1002 " --> pdb=" O ASP C 998 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 20 Processing helix chain 'D' and resid 25 through 43 removed outlier: 5.218A pdb=" N ALA D 30 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ALA D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE D 32 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 95 removed outlier: 3.501A pdb=" N GLN D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS D 93 " --> pdb=" O ASP D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 141 Processing helix chain 'D' and resid 145 through 177 Proline residue: D 162 - end of helix removed outlier: 3.878A pdb=" N GLU D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN D 177 " --> pdb=" O ASP D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 removed outlier: 3.674A pdb=" N GLU D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 218 Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 233 through 245 removed outlier: 4.016A pdb=" N PHE D 245 " --> pdb=" O LEU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 259 Processing helix chain 'D' and resid 261 through 269 removed outlier: 4.732A pdb=" N ILE D 265 " --> pdb=" O TYR D 261 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 291 removed outlier: 4.590A pdb=" N ARG D 280 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU D 282 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 301 Processing helix chain 'D' and resid 308 through 324 Processing helix chain 'D' and resid 349 through 354 Processing helix chain 'D' and resid 357 through 366 removed outlier: 4.380A pdb=" N GLU D 361 " --> pdb=" O LYS D 357 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLN D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 392 Processing helix chain 'D' and resid 428 through 439 Processing helix chain 'D' and resid 471 through 476 Processing helix chain 'D' and resid 478 through 481 No H-bonds generated for 'chain 'D' and resid 478 through 481' Processing helix chain 'D' and resid 492 through 503 Processing helix chain 'D' and resid 516 through 519 Processing helix chain 'D' and resid 523 through 533 removed outlier: 4.143A pdb=" N GLY D 526 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL D 531 " --> pdb=" O ARG D 528 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL D 532 " --> pdb=" O LYS D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 Processing helix chain 'D' and resid 601 through 610 Processing helix chain 'D' and resid 613 through 615 No H-bonds generated for 'chain 'D' and resid 613 through 615' Processing helix chain 'D' and resid 647 through 650 No H-bonds generated for 'chain 'D' and resid 647 through 650' Processing helix chain 'D' and resid 675 through 678 No H-bonds generated for 'chain 'D' and resid 675 through 678' Processing helix chain 'D' and resid 683 through 702 removed outlier: 4.067A pdb=" N ASP D 688 " --> pdb=" O ASP D 684 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS D 702 " --> pdb=" O ASN D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 709 Processing helix chain 'D' and resid 721 through 729 Processing helix chain 'D' and resid 771 through 773 No H-bonds generated for 'chain 'D' and resid 771 through 773' Processing helix chain 'D' and resid 828 through 837 removed outlier: 4.088A pdb=" N THR D 836 " --> pdb=" O LYS D 832 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS D 837 " --> pdb=" O ALA D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 856 removed outlier: 3.698A pdb=" N HIS D 850 " --> pdb=" O GLU D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 859 through 864 Processing helix chain 'D' and resid 866 through 870 Processing helix chain 'D' and resid 883 through 897 Processing helix chain 'D' and resid 899 through 901 No H-bonds generated for 'chain 'D' and resid 899 through 901' Processing helix chain 'D' and resid 919 through 926 Processing helix chain 'D' and resid 957 through 961 Processing helix chain 'D' and resid 969 through 977 removed outlier: 3.547A pdb=" N VAL D 973 " --> pdb=" O ALA D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 988 No H-bonds generated for 'chain 'D' and resid 985 through 988' Processing helix chain 'D' and resid 1000 through 1023 Processing sheet with id= A, first strand: chain 'A' and resid 46 through 48 removed outlier: 3.739A pdb=" N GLY A 76 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN A 103 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A 122 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLN A 116 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 402 through 404 removed outlier: 8.750A pdb=" N VAL A 403 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N CYS A 370 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 337 " --> pdb=" O HIS A 369 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ASN A 371 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP A 339 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU A 338 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE A 445 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 508 through 515 removed outlier: 6.199A pdb=" N LYS A 589 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE A 540 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TRP A 591 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ASP A 542 " --> pdb=" O TRP A 591 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS A 593 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE A 590 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 793 through 796 Processing sheet with id= E, first strand: chain 'A' and resid 814 through 816 Processing sheet with id= F, first strand: chain 'A' and resid 908 through 911 Processing sheet with id= G, first strand: chain 'A' and resid 740 through 746 removed outlier: 6.928A pdb=" N ASP A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 931 through 934 removed outlier: 4.564A pdb=" N ALA A 943 " --> pdb=" O GLN A 933 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 49 removed outlier: 5.809A pdb=" N ASN B 103 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 104 " --> pdb=" O MET B 115 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 122 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN B 116 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLU B 120 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 337 through 339 Processing sheet with id= K, first strand: chain 'B' and resid 444 through 447 removed outlier: 7.107A pdb=" N ILE B 509 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLY B 447 " --> pdb=" O ILE B 509 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA B 511 " --> pdb=" O GLY B 447 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS B 589 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE B 540 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP B 591 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASP B 542 " --> pdb=" O TRP B 591 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N HIS B 593 " --> pdb=" O ASP B 542 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE B 590 " --> pdb=" O ILE B 621 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 793 through 796 Processing sheet with id= M, first strand: chain 'B' and resid 814 through 816 Processing sheet with id= N, first strand: chain 'B' and resid 908 through 911 Processing sheet with id= O, first strand: chain 'B' and resid 740 through 746 removed outlier: 6.853A pdb=" N ASP B 749 " --> pdb=" O TYR B 745 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 931 through 934 removed outlier: 4.673A pdb=" N ALA B 943 " --> pdb=" O GLN B 933 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 46 through 49 Processing sheet with id= R, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= S, first strand: chain 'C' and resid 77 through 80 removed outlier: 6.301A pdb=" N GLN C 116 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 368 through 370 removed outlier: 6.256A pdb=" N ILE C 337 " --> pdb=" O HIS C 369 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU C 338 " --> pdb=" O ARG C 443 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE C 445 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE C 509 " --> pdb=" O ILE C 445 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLY C 447 " --> pdb=" O ILE C 509 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA C 511 " --> pdb=" O GLY C 447 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 508 " --> pdb=" O ARG C 577 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LYS C 589 " --> pdb=" O ILE C 538 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE C 540 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TRP C 591 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASP C 542 " --> pdb=" O TRP C 591 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS C 593 " --> pdb=" O ASP C 542 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE C 590 " --> pdb=" O ILE C 621 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 666 through 668 Processing sheet with id= V, first strand: chain 'C' and resid 740 through 746 removed outlier: 6.793A pdb=" N ASP C 749 " --> pdb=" O TYR C 745 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 931 through 935 removed outlier: 3.515A pdb=" N LYS C 931 " --> pdb=" O GLU C 945 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA C 943 " --> pdb=" O GLN C 933 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASP C 935 " --> pdb=" O THR C 941 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N THR C 941 " --> pdb=" O ASP C 935 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 46 through 49 removed outlier: 5.183A pdb=" N ASN D 103 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN D 122 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLN D 116 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLU D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 51 through 54 removed outlier: 4.084A pdb=" N VAL D 51 " --> pdb=" O PRO D 63 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 402 through 404 removed outlier: 8.463A pdb=" N VAL D 403 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N CYS D 370 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE D 337 " --> pdb=" O HIS D 369 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ASN D 371 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASP D 339 " --> pdb=" O ASN D 371 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU D 338 " --> pdb=" O ARG D 443 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE D 445 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE D 509 " --> pdb=" O ILE D 445 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N GLY D 447 " --> pdb=" O ILE D 509 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA D 511 " --> pdb=" O GLY D 447 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL D 572 " --> pdb=" O ASP D 542 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASP D 542 " --> pdb=" O VAL D 572 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N PHE D 574 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE D 540 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL D 576 " --> pdb=" O ILE D 538 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE D 538 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS D 589 " --> pdb=" O ILE D 538 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE D 540 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP D 591 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ASP D 542 " --> pdb=" O TRP D 591 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE D 590 " --> pdb=" O ILE D 621 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 666 through 668 Processing sheet with id= AB, first strand: chain 'D' and resid 779 through 782 Processing sheet with id= AC, first strand: chain 'D' and resid 814 through 816 Processing sheet with id= AD, first strand: chain 'D' and resid 741 through 746 removed outlier: 3.857A pdb=" N TYR D 745 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ASP D 749 " --> pdb=" O TYR D 745 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 931 through 935 removed outlier: 4.303A pdb=" N ALA D 943 " --> pdb=" O GLN D 933 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ASP D 935 " --> pdb=" O THR D 941 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR D 941 " --> pdb=" O ASP D 935 " (cutoff:3.500A) 1294 hydrogen bonds defined for protein. 3696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 236 hydrogen bonds 472 hydrogen bond angles 0 basepair planarities 87 basepair parallelities 180 stacking parallelities Total time for adding SS restraints: 18.85 Time building geometry restraints manager: 17.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5945 1.31 - 1.44: 11195 1.44 - 1.56: 20977 1.56 - 1.69: 425 1.69 - 1.81: 160 Bond restraints: 38702 Sorted by residual: bond pdb=" C ILE C 987 " pdb=" N ARG C 988 " ideal model delta sigma weight residual 1.335 1.439 -0.104 1.31e-02 5.83e+03 6.36e+01 bond pdb=" C SER A 2 " pdb=" N LEU A 3 " ideal model delta sigma weight residual 1.335 1.423 -0.088 1.31e-02 5.83e+03 4.49e+01 bond pdb=" C PRO A 449 " pdb=" O PRO A 449 " ideal model delta sigma weight residual 1.246 1.192 0.054 8.50e-03 1.38e+04 3.98e+01 bond pdb=" C SER C 74 " pdb=" N ARG C 75 " ideal model delta sigma weight residual 1.334 1.238 0.096 1.58e-02 4.01e+03 3.72e+01 bond pdb=" C VAL B 442 " pdb=" N ARG B 443 " ideal model delta sigma weight residual 1.332 1.414 -0.082 1.35e-02 5.49e+03 3.69e+01 ... (remaining 38697 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.35: 1705 105.35 - 112.68: 18411 112.68 - 120.01: 18733 120.01 - 127.34: 13704 127.34 - 134.68: 690 Bond angle restraints: 53243 Sorted by residual: angle pdb=" N ASN B 548 " pdb=" CA ASN B 548 " pdb=" C ASN B 548 " ideal model delta sigma weight residual 112.97 104.15 8.82 1.06e+00 8.90e-01 6.92e+01 angle pdb=" N ARG C 522 " pdb=" CA ARG C 522 " pdb=" C ARG C 522 " ideal model delta sigma weight residual 114.04 104.09 9.95 1.24e+00 6.50e-01 6.44e+01 angle pdb=" O3' DC G 23 " pdb=" C3' DC G 23 " pdb=" C2' DC G 23 " ideal model delta sigma weight residual 111.50 99.69 11.81 1.50e+00 4.44e-01 6.20e+01 angle pdb=" N ASN C 548 " pdb=" CA ASN C 548 " pdb=" C ASN C 548 " ideal model delta sigma weight residual 112.97 104.89 8.08 1.06e+00 8.90e-01 5.81e+01 angle pdb=" N ASP B 638 " pdb=" CA ASP B 638 " pdb=" C ASP B 638 " ideal model delta sigma weight residual 112.57 104.25 8.32 1.13e+00 7.83e-01 5.43e+01 ... (remaining 53238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 20292 35.94 - 71.87: 2405 71.87 - 107.81: 74 107.81 - 143.74: 4 143.74 - 179.68: 6 Dihedral angle restraints: 22781 sinusoidal: 10863 harmonic: 11918 Sorted by residual: dihedral pdb=" C GLU C 506 " pdb=" N GLU C 506 " pdb=" CA GLU C 506 " pdb=" CB GLU C 506 " ideal model delta harmonic sigma weight residual -122.60 -136.40 13.80 0 2.50e+00 1.60e-01 3.05e+01 dihedral pdb=" C CYS A 370 " pdb=" N CYS A 370 " pdb=" CA CYS A 370 " pdb=" CB CYS A 370 " ideal model delta harmonic sigma weight residual -122.60 -110.02 -12.58 0 2.50e+00 1.60e-01 2.53e+01 dihedral pdb=" C THR A 318 " pdb=" N THR A 318 " pdb=" CA THR A 318 " pdb=" CB THR A 318 " ideal model delta harmonic sigma weight residual -122.00 -134.15 12.15 0 2.50e+00 1.60e-01 2.36e+01 ... (remaining 22778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3249 0.094 - 0.188: 1991 0.188 - 0.282: 439 0.282 - 0.376: 52 0.376 - 0.470: 8 Chirality restraints: 5739 Sorted by residual: chirality pdb=" C3' DT L 27 " pdb=" C4' DT L 27 " pdb=" O3' DT L 27 " pdb=" C2' DT L 27 " both_signs ideal model delta sigma weight residual False -2.66 -2.19 -0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" CA GLU C 506 " pdb=" N GLU C 506 " pdb=" C GLU C 506 " pdb=" CB GLU C 506 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" C3' DT J 27 " pdb=" C4' DT J 27 " pdb=" O3' DT J 27 " pdb=" C2' DT J 27 " both_signs ideal model delta sigma weight residual False -2.66 -2.24 -0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 5736 not shown) Planarity restraints: 6185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 925 " 0.024 2.00e-02 2.50e+03 4.91e-02 2.42e+01 pdb=" C ALA B 925 " -0.085 2.00e-02 2.50e+03 pdb=" O ALA B 925 " 0.032 2.00e-02 2.50e+03 pdb=" N LYS B 926 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 756 " -0.022 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C SER D 756 " 0.078 2.00e-02 2.50e+03 pdb=" O SER D 756 " -0.029 2.00e-02 2.50e+03 pdb=" N LYS D 757 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 937 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C ALA C 937 " 0.063 2.00e-02 2.50e+03 pdb=" O ALA C 937 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS C 938 " -0.022 2.00e-02 2.50e+03 ... (remaining 6182 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 66 2.43 - 3.05: 22496 3.05 - 3.67: 58062 3.67 - 4.28: 99187 4.28 - 4.90: 149021 Nonbonded interactions: 328832 Sorted by model distance: nonbonded pdb=" OD2 ASP B 64 " pdb="CA CA B1102 " model vdw 1.819 2.510 nonbonded pdb=" OE2 GLU A 79 " pdb="CA CA A1102 " model vdw 1.832 2.510 nonbonded pdb=" OE2 GLU D 25 " pdb="CA CA D1101 " model vdw 1.916 2.510 nonbonded pdb=" OE2 GLU B 25 " pdb="CA CA B1102 " model vdw 1.941 2.510 nonbonded pdb=" OE2 GLU B 79 " pdb="CA CA B1102 " model vdw 2.007 2.510 ... (remaining 328827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 411 or resid 421 through 578 or resid 587 throug \ h 839 or resid 843 through 1029)) selection = (chain 'B' and (resid 2 through 411 or resid 421 through 839 or resid 843 throug \ h 1029)) selection = (chain 'C' and (resid 2 through 411 or resid 421 through 578 or resid 587 throug \ h 839 or resid 843 through 1029)) selection = (chain 'D' and (resid 2 through 411 or resid 421 through 578 or resid 587 throug \ h 1029)) } ncs_group { reference = (chain 'E' and resid 1 through 25) selection = (chain 'G' and resid 1 through 25) selection = (chain 'I' and resid 1 through 25) selection = chain 'K' } ncs_group { reference = (chain 'F' and resid 4 through 28) selection = (chain 'H' and resid 4 through 28) selection = (chain 'J' and resid 4 through 28) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.220 Construct map_model_manager: 0.020 Extract box with map and model: 29.750 Check model and map are aligned: 0.590 Set scattering table: 0.330 Process input model: 117.250 Find NCS groups from input model: 3.460 Set up NCS constraints: 0.210 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: 0.010 Load rotamer database and sin/cos tables:13.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 : 0.011 0.104 38702 Z= 0.729 Angle : 1.602 11.807 53243 Z= 1.190 Chirality : 0.113 0.470 5739 Planarity : 0.005 0.128 6185 Dihedral : 24.100 179.676 15085 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.45 % Favored : 93.40 % Rotamer: Outliers : 12.88 % Allowed : 16.74 % Favored : 70.37 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 2.44 % 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: -3.88 (0.11), residues: 4029 helix: -2.59 (0.09), residues: 1937 sheet: -2.04 (0.24), residues: 364 loop : -2.51 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 960 HIS 0.006 0.001 HIS B 537 PHE 0.020 0.003 PHE D 770 TYR 0.033 0.003 TYR C 286 ARG 0.017 0.001 ARG D 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 444 poor density : 587 time to evaluate : 4.099 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: A 59 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7595 (p0) REVERT: A 126 MET cc_start: 0.8717 (mmm) cc_final: 0.8192 (mtm) REVERT: A 208 MET cc_start: 0.9095 (mtt) cc_final: 0.8840 (mtt) REVERT: A 318 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8872 (t) REVERT: A 329 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7428 (tm-30) REVERT: A 560 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8874 (t0) REVERT: A 651 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8480 (mmtt) REVERT: A 709 MET cc_start: 0.9329 (mmt) cc_final: 0.9033 (mmm) REVERT: A 719 MET cc_start: 0.9176 (mmm) cc_final: 0.8943 (mmp) REVERT: A 893 MET cc_start: 0.8030 (ttm) cc_final: 0.7696 (ttp) REVERT: B 3 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8528 (tt) REVERT: B 73 GLN cc_start: 0.8292 (mt0) cc_final: 0.7908 (mt0) REVERT: B 215 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8915 (p) REVERT: B 367 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: B 633 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.7959 (m) REVERT: B 719 MET cc_start: 0.9134 (mmm) cc_final: 0.8794 (mmm) REVERT: B 881 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: C 534 ASP cc_start: 0.8148 (m-30) cc_final: 0.7703 (m-30) REVERT: C 654 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7711 (mtmm) REVERT: C 696 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8409 (mmm160) REVERT: C 864 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8791 (tptt) REVERT: C 1024 MET cc_start: 0.7762 (mtt) cc_final: 0.7352 (mtt) REVERT: D 14 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7295 (mp0) REVERT: D 69 ASP cc_start: 0.7084 (t0) cc_final: 0.6447 (p0) REVERT: D 83 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6668 (mm-30) REVERT: D 167 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6673 (mm) REVERT: D 191 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7099 (tp) REVERT: D 200 PHE cc_start: 0.7255 (t80) cc_final: 0.7037 (t80) REVERT: D 234 ILE cc_start: 0.5497 (mm) cc_final: 0.5257 (mp) REVERT: D 333 LYS cc_start: 0.7778 (mttt) cc_final: 0.7333 (mppt) REVERT: D 335 VAL cc_start: 0.7886 (OUTLIER) cc_final: 0.7601 (p) REVERT: D 370 CYS cc_start: 0.6303 (OUTLIER) cc_final: 0.5470 (p) REVERT: D 422 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6570 (mt) REVERT: D 433 ARG cc_start: 0.3662 (OUTLIER) cc_final: 0.2611 (mtm180) REVERT: D 451 TYR cc_start: 0.1545 (OUTLIER) cc_final: 0.1335 (m-80) REVERT: D 473 ARG cc_start: 0.5912 (OUTLIER) cc_final: 0.5639 (mtp180) REVERT: D 505 LYS cc_start: 0.8852 (tttt) cc_final: 0.8513 (mmtm) REVERT: D 534 ASP cc_start: 0.6753 (m-30) cc_final: 0.6548 (m-30) REVERT: D 543 MET cc_start: 0.6727 (mmm) cc_final: 0.6520 (mmm) REVERT: D 544 LYS cc_start: 0.5909 (OUTLIER) cc_final: 0.5620 (mttt) REVERT: D 693 PHE cc_start: 0.8505 (t80) cc_final: 0.8093 (t80) REVERT: D 700 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8558 (tp) REVERT: D 835 GLN cc_start: 0.6530 (OUTLIER) cc_final: 0.6182 (tm-30) REVERT: D 843 ILE cc_start: 0.2708 (OUTLIER) cc_final: 0.2049 (mp) REVERT: D 892 LEU cc_start: 0.5736 (OUTLIER) cc_final: 0.5456 (mt) REVERT: D 944 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8055 (t) REVERT: D 986 THR cc_start: 0.6397 (OUTLIER) cc_final: 0.5856 (p) REVERT: D 1016 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8310 (tm-30) outliers start: 444 outliers final: 42 residues processed: 923 average time/residue: 1.9214 time to fit residues: 2056.6447 Evaluate side-chains 293 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 222 time to evaluate : 4.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 950 THR Chi-restraints excluded: chain B residue 1015 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 654 LYS Chi-restraints excluded: chain C residue 696 ARG Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 950 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 433 ARG Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 544 LYS Chi-restraints excluded: chain D residue 609 LYS Chi-restraints excluded: chain D residue 654 LYS Chi-restraints excluded: chain D residue 700 ILE Chi-restraints excluded: chain D residue 716 ASP Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 835 GLN Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain D residue 844 SER Chi-restraints excluded: chain D residue 892 LEU Chi-restraints excluded: chain D residue 931 LYS Chi-restraints excluded: chain D residue 944 VAL Chi-restraints excluded: chain D residue 986 THR Chi-restraints excluded: chain D residue 993 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 1.9990 chunk 318 optimal weight: 0.9990 chunk 176 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 214 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 chunk 245 optimal weight: 0.7980 chunk 381 optimal weight: 4.9990 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 24 ASN A 33 GLN A 116 GLN A 122 GLN A 279 GLN A 410 ASN A 448 ASN A 537 HIS A 627 HIS A 628 ASN A 728 GLN A 896 HIS B 10 GLN B 116 GLN B 122 GLN B 371 ASN B 437 GLN B 448 ASN B 565 GLN B 628 ASN B 857 HIS B 896 HIS C 33 GLN C 59 ASN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 HIS C 212 HIS C 236 GLN C 325 HIS ** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN C 560 ASN C 563 ASN C 565 GLN C 728 GLN C 792 GLN C 858 HIS D 10 GLN D 24 ASN D 211 GLN D 266 GLN D 294 ASN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 ASN ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 ASN D 448 ASN D 628 ASN D 760 ASN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 835 GLN ** D 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 38702 Z= 0.236 Angle : 0.650 11.884 53243 Z= 0.352 Chirality : 0.042 0.377 5739 Planarity : 0.005 0.072 6185 Dihedral : 23.975 179.159 7053 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.59 % Allowed : 24.64 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.77 (0.12), residues: 4029 helix: -0.43 (0.11), residues: 1924 sheet: -1.53 (0.24), residues: 399 loop : -1.87 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 885 HIS 0.009 0.001 HIS D 837 PHE 0.016 0.001 PHE D 878 TYR 0.021 0.002 TYR C 838 ARG 0.008 0.001 ARG D 967 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 242 time to evaluate : 4.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7636 (p0) REVERT: A 208 MET cc_start: 0.9093 (mtt) cc_final: 0.8869 (mtt) REVERT: A 224 ASP cc_start: 0.7701 (t0) cc_final: 0.7342 (t0) REVERT: A 259 LYS cc_start: 0.9038 (tppt) cc_final: 0.8713 (tppp) REVERT: A 318 THR cc_start: 0.9156 (t) cc_final: 0.8910 (t) REVERT: A 329 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: A 492 MET cc_start: 0.8890 (mmm) cc_final: 0.8663 (mmp) REVERT: A 656 LEU cc_start: 0.8890 (tt) cc_final: 0.8686 (tm) REVERT: A 709 MET cc_start: 0.9346 (mmt) cc_final: 0.8990 (mmm) REVERT: A 863 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7966 (pt0) REVERT: B 23 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7464 (mtp180) REVERT: B 126 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8699 (mtm) REVERT: B 152 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8708 (ttmm) REVERT: B 215 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8650 (p) REVERT: B 277 GLU cc_start: 0.7982 (tp30) cc_final: 0.7302 (tp30) REVERT: B 291 ARG cc_start: 0.8298 (mpt-90) cc_final: 0.8091 (mpt-90) REVERT: B 367 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: B 652 GLN cc_start: 0.7578 (pp30) cc_final: 0.7339 (pp30) REVERT: B 719 MET cc_start: 0.9062 (mmm) cc_final: 0.8817 (mmm) REVERT: B 881 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: B 990 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8835 (mttm) REVERT: B 1029 MET cc_start: 0.7073 (mtp) cc_final: 0.6806 (mtp) REVERT: C 203 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7621 (ttp80) REVERT: C 245 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7747 (p90) REVERT: C 602 ARG cc_start: 0.7786 (ptp90) cc_final: 0.7480 (ptp90) REVERT: C 612 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8305 (mmmt) REVERT: C 654 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7792 (mtmm) REVERT: C 709 MET cc_start: 0.8542 (mpp) cc_final: 0.8176 (mpp) REVERT: D 14 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7454 (mp0) REVERT: D 241 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5385 (mm) REVERT: D 333 LYS cc_start: 0.7732 (mttt) cc_final: 0.7239 (mppt) REVERT: D 642 PHE cc_start: 0.7879 (m-80) cc_final: 0.7653 (m-10) REVERT: D 693 PHE cc_start: 0.8457 (t80) cc_final: 0.8063 (t80) REVERT: D 1016 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8306 (tm-30) outliers start: 158 outliers final: 50 residues processed: 373 average time/residue: 1.5968 time to fit residues: 715.1639 Evaluate side-chains 244 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 179 time to evaluate : 4.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 260 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 990 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 612 LYS Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 654 LYS Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 796 THR Chi-restraints excluded: chain C residue 803 ASP Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 809 GLN Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 993 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 211 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 317 optimal weight: 0.9990 chunk 259 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 382 optimal weight: 2.9990 chunk 412 optimal weight: 4.9990 chunk 340 optimal weight: 0.9990 chunk 378 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 163 HIS A 239 GLN A 673 ASN B 4 GLN B 73 GLN B 229 HIS ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 ASN D 437 GLN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 858 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 38702 Z= 0.213 Angle : 0.560 11.254 53243 Z= 0.304 Chirality : 0.040 0.313 5739 Planarity : 0.004 0.050 6185 Dihedral : 23.425 179.855 6952 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.69 % Allowed : 25.74 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.86 (0.13), residues: 4029 helix: 0.41 (0.12), residues: 1917 sheet: -1.10 (0.24), residues: 402 loop : -1.53 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 639 HIS 0.010 0.001 HIS D 850 PHE 0.029 0.001 PHE D 200 TYR 0.022 0.001 TYR D 829 ARG 0.006 0.000 ARG D 967 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 217 time to evaluate : 4.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6782 (tm-30) REVERT: A 208 MET cc_start: 0.9073 (mtt) cc_final: 0.8783 (mtt) REVERT: A 224 ASP cc_start: 0.7703 (t0) cc_final: 0.7293 (t0) REVERT: A 259 LYS cc_start: 0.9004 (tppt) cc_final: 0.8596 (tppp) REVERT: A 291 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7768 (ttm-80) REVERT: A 642 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6911 (m-80) REVERT: A 656 LEU cc_start: 0.8872 (tt) cc_final: 0.8672 (tm) REVERT: B 126 MET cc_start: 0.9117 (mtm) cc_final: 0.8906 (mtm) REVERT: B 277 GLU cc_start: 0.8075 (tp30) cc_final: 0.7356 (tp30) REVERT: B 291 ARG cc_start: 0.8292 (mpt-90) cc_final: 0.7913 (mpt-90) REVERT: B 319 ASP cc_start: 0.8684 (t70) cc_final: 0.8457 (t0) REVERT: B 367 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: B 719 MET cc_start: 0.9033 (mmm) cc_final: 0.8757 (mmm) REVERT: B 881 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: C 203 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7629 (ttp80) REVERT: C 245 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7794 (p90) REVERT: C 336 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8266 (mm-30) REVERT: C 602 ARG cc_start: 0.7823 (ptp90) cc_final: 0.7424 (ptp90) REVERT: C 641 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7131 (mt-10) REVERT: C 654 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7891 (mtmm) REVERT: D 14 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7461 (mp0) REVERT: D 333 LYS cc_start: 0.7717 (mttt) cc_final: 0.7267 (mppt) REVERT: D 693 PHE cc_start: 0.8617 (t80) cc_final: 0.8415 (t80) REVERT: D 905 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.6982 (m-80) REVERT: D 1016 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8267 (tm-30) outliers start: 127 outliers final: 49 residues processed: 319 average time/residue: 1.5521 time to fit residues: 599.3249 Evaluate side-chains 228 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 169 time to evaluate : 4.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 654 LYS Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 796 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 809 GLN Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 905 TYR Chi-restraints excluded: chain D residue 993 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 377 optimal weight: 8.9990 chunk 287 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 256 optimal weight: 0.1980 chunk 383 optimal weight: 8.9990 chunk 405 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 363 optimal weight: 2.9990 chunk 109 optimal weight: 0.0980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN B 73 GLN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 GLN D 288 ASN D 437 GLN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 858 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 38702 Z= 0.218 Angle : 0.547 15.251 53243 Z= 0.293 Chirality : 0.039 0.213 5739 Planarity : 0.004 0.070 6185 Dihedral : 23.110 178.977 6944 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.00 % Allowed : 25.07 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.44 (0.13), residues: 4029 helix: 0.73 (0.12), residues: 1917 sheet: -0.75 (0.24), residues: 418 loop : -1.33 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 639 HIS 0.006 0.001 HIS D 850 PHE 0.022 0.001 PHE A 882 TYR 0.019 0.001 TYR D 829 ARG 0.009 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 199 time to evaluate : 4.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7171 (tm-30) cc_final: 0.6955 (tm-30) REVERT: A 208 MET cc_start: 0.9063 (mtt) cc_final: 0.8771 (mtt) REVERT: A 224 ASP cc_start: 0.7696 (t0) cc_final: 0.7285 (t0) REVERT: A 259 LYS cc_start: 0.9017 (tppt) cc_final: 0.8693 (tppp) REVERT: A 329 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: A 642 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.6912 (m-80) REVERT: A 708 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8868 (mp) REVERT: A 1029 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6928 (mtp) REVERT: B 107 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6816 (tm-30) REVERT: B 109 SER cc_start: 0.8429 (m) cc_final: 0.8132 (t) REVERT: B 128 ASP cc_start: 0.8628 (t70) cc_final: 0.8393 (t0) REVERT: B 277 GLU cc_start: 0.8138 (tp30) cc_final: 0.7415 (tp30) REVERT: B 291 ARG cc_start: 0.8296 (mpt-90) cc_final: 0.8012 (mpt-90) REVERT: B 319 ASP cc_start: 0.8718 (t70) cc_final: 0.8497 (t0) REVERT: B 367 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: B 719 MET cc_start: 0.9013 (mmm) cc_final: 0.8770 (mmm) REVERT: B 881 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: C 107 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7589 (tm-30) REVERT: C 245 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7813 (p90) REVERT: C 327 GLN cc_start: 0.8784 (mp10) cc_final: 0.8235 (mp10) REVERT: C 336 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8230 (mm-30) REVERT: C 366 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8092 (pt0) REVERT: C 602 ARG cc_start: 0.7782 (ptp90) cc_final: 0.7440 (ptp90) REVERT: C 753 MET cc_start: 0.7511 (tmm) cc_final: 0.7273 (tmm) REVERT: C 885 TRP cc_start: 0.7301 (m100) cc_final: 0.6798 (m100) REVERT: C 931 LYS cc_start: 0.8374 (mttt) cc_final: 0.8115 (ptpp) REVERT: C 1024 MET cc_start: 0.7632 (mmt) cc_final: 0.7358 (mmt) REVERT: D 14 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7443 (mp0) REVERT: D 115 MET cc_start: 0.7091 (mtp) cc_final: 0.6704 (ttm) REVERT: D 333 LYS cc_start: 0.7742 (mttt) cc_final: 0.7451 (mmmt) REVERT: D 751 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6992 (tp) REVERT: D 754 TYR cc_start: 0.6366 (t80) cc_final: 0.6134 (t80) outliers start: 138 outliers final: 61 residues processed: 318 average time/residue: 1.6480 time to fit residues: 632.1545 Evaluate side-chains 240 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 167 time to evaluate : 4.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 719 MET Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 818 MET Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 809 GLN Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 905 TYR Chi-restraints excluded: chain D residue 931 LYS Chi-restraints excluded: chain D residue 950 THR Chi-restraints excluded: chain D residue 993 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 338 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 302 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 346 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 364 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN B 232 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 HIS B 371 ASN B 382 ASN B 437 GLN B 632 GLN ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN C 371 ASN C 437 GLN C 438 ASN C 658 GLN D 53 GLN ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN D 565 GLN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 38702 Z= 0.341 Angle : 0.585 10.830 53243 Z= 0.313 Chirality : 0.042 0.179 5739 Planarity : 0.004 0.048 6185 Dihedral : 23.109 179.648 6939 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.35 % Allowed : 24.38 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 4029 helix: 0.74 (0.12), residues: 1925 sheet: -0.53 (0.24), residues: 425 loop : -1.31 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 639 HIS 0.005 0.001 HIS B 837 PHE 0.022 0.002 PHE D 878 TYR 0.019 0.002 TYR D 829 ARG 0.009 0.001 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 178 time to evaluate : 4.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ASP cc_start: 0.7762 (t0) cc_final: 0.7353 (t0) REVERT: A 259 LYS cc_start: 0.9084 (tppt) cc_final: 0.8760 (tppp) REVERT: A 329 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7515 (tm-30) REVERT: A 642 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.7013 (m-80) REVERT: A 708 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8950 (mp) REVERT: B 107 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: B 277 GLU cc_start: 0.8377 (tp30) cc_final: 0.7535 (tp30) REVERT: B 319 ASP cc_start: 0.8763 (t70) cc_final: 0.8535 (t0) REVERT: B 367 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: B 635 GLU cc_start: 0.7499 (tp30) cc_final: 0.7294 (tp30) REVERT: B 719 MET cc_start: 0.9020 (mmm) cc_final: 0.8807 (mmm) REVERT: B 819 ASN cc_start: 0.7805 (p0) cc_final: 0.7508 (p0) REVERT: B 881 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: C 107 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: C 245 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8160 (p90) REVERT: C 327 GLN cc_start: 0.8913 (mp10) cc_final: 0.8593 (mp10) REVERT: C 336 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8264 (mm-30) REVERT: C 472 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8104 (ptp-170) REVERT: C 602 ARG cc_start: 0.7788 (ptp90) cc_final: 0.7570 (pmm150) REVERT: C 753 MET cc_start: 0.7609 (tmm) cc_final: 0.7375 (tmm) REVERT: D 14 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7384 (mp0) REVERT: D 115 MET cc_start: 0.7219 (mtp) cc_final: 0.6717 (ttm) REVERT: D 333 LYS cc_start: 0.7723 (mttt) cc_final: 0.7301 (mppt) REVERT: D 728 GLN cc_start: 0.7303 (mt0) cc_final: 0.7048 (mm-40) outliers start: 150 outliers final: 77 residues processed: 303 average time/residue: 1.5468 time to fit residues: 565.4785 Evaluate side-chains 246 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 159 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 451 TYR Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 719 MET Chi-restraints excluded: chain C residue 737 LYS Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 796 THR Chi-restraints excluded: chain C residue 803 ASP Chi-restraints excluded: chain C residue 818 MET Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 947 ASP Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain C residue 1017 THR Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 809 GLN Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 905 TYR Chi-restraints excluded: chain D residue 931 LYS Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 1028 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 136 optimal weight: 0.9980 chunk 365 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 238 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 406 optimal weight: 3.9990 chunk 337 optimal weight: 0.3980 chunk 188 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 213 optimal weight: 0.0870 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN B 437 GLN B 537 HIS C 462 ASN ** D 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38702 Z= 0.171 Angle : 0.523 12.248 53243 Z= 0.279 Chirality : 0.038 0.160 5739 Planarity : 0.004 0.053 6185 Dihedral : 22.849 179.201 6939 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.34 % Allowed : 25.39 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 (0.13), residues: 4029 helix: 0.98 (0.12), residues: 1914 sheet: -0.35 (0.24), residues: 418 loop : -1.20 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 885 HIS 0.004 0.001 HIS D 850 PHE 0.017 0.001 PHE D 878 TYR 0.016 0.001 TYR D 994 ARG 0.008 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 185 time to evaluate : 4.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6940 (tm-30) REVERT: A 208 MET cc_start: 0.9062 (mtt) cc_final: 0.8790 (mtt) REVERT: A 224 ASP cc_start: 0.7684 (t0) cc_final: 0.7402 (t0) REVERT: A 259 LYS cc_start: 0.9004 (tppt) cc_final: 0.8563 (tppp) REVERT: A 329 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: A 642 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.7031 (m-80) REVERT: A 708 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8938 (mp) REVERT: A 828 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8420 (m-30) REVERT: A 908 LYS cc_start: 0.8417 (tmmt) cc_final: 0.8151 (tmmt) REVERT: B 107 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6724 (tm-30) REVERT: B 277 GLU cc_start: 0.8196 (tp30) cc_final: 0.7370 (tp30) REVERT: B 367 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: B 719 MET cc_start: 0.8974 (mmm) cc_final: 0.8724 (mmm) REVERT: B 818 MET cc_start: 0.7496 (tmm) cc_final: 0.6906 (tmm) REVERT: B 819 ASN cc_start: 0.7845 (p0) cc_final: 0.7394 (p0) REVERT: B 881 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: B 1029 MET cc_start: 0.6308 (mtp) cc_final: 0.6107 (mtm) REVERT: C 107 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: C 245 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8189 (p90) REVERT: C 336 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8336 (mm-30) REVERT: C 472 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8125 (ptp-170) REVERT: C 602 ARG cc_start: 0.7772 (ptp90) cc_final: 0.7510 (ptp90) REVERT: C 652 GLN cc_start: 0.8458 (mm-40) cc_final: 0.7998 (tm-30) REVERT: C 893 MET cc_start: 0.6475 (ttp) cc_final: 0.6236 (ttp) REVERT: D 14 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7405 (mp0) REVERT: D 115 MET cc_start: 0.7152 (mtp) cc_final: 0.6713 (ttm) REVERT: D 333 LYS cc_start: 0.7772 (mttt) cc_final: 0.7314 (mppt) REVERT: D 728 GLN cc_start: 0.7285 (mt0) cc_final: 0.7036 (mm-40) REVERT: D 1016 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8178 (tm-30) outliers start: 115 outliers final: 62 residues processed: 285 average time/residue: 1.5998 time to fit residues: 549.8960 Evaluate side-chains 239 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 166 time to evaluate : 4.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 719 MET Chi-restraints excluded: chain C residue 737 LYS Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 809 GLN Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 905 TYR Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 1028 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 391 optimal weight: 0.2980 chunk 45 optimal weight: 0.1980 chunk 231 optimal weight: 0.8980 chunk 296 optimal weight: 0.0070 chunk 229 optimal weight: 0.8980 chunk 342 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 404 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 246 optimal weight: 0.3980 chunk 186 optimal weight: 0.4980 overall best weight: 0.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN D 652 GLN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 858 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 38702 Z= 0.142 Angle : 0.507 11.265 53243 Z= 0.269 Chirality : 0.037 0.198 5739 Planarity : 0.004 0.064 6185 Dihedral : 22.486 178.920 6937 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.02 % Allowed : 25.62 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 (0.13), residues: 4029 helix: 1.15 (0.12), residues: 1924 sheet: -0.22 (0.25), residues: 412 loop : -1.10 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 885 HIS 0.005 0.000 HIS D 850 PHE 0.016 0.001 PHE D 878 TYR 0.016 0.001 TYR D 181 ARG 0.011 0.000 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 193 time to evaluate : 4.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7267 (tm-30) cc_final: 0.7037 (tm-30) REVERT: A 126 MET cc_start: 0.8761 (mtp) cc_final: 0.8539 (mtm) REVERT: A 128 ASP cc_start: 0.7920 (t0) cc_final: 0.7678 (t0) REVERT: A 208 MET cc_start: 0.9055 (mtt) cc_final: 0.8763 (mtt) REVERT: A 224 ASP cc_start: 0.7614 (t0) cc_final: 0.7351 (t0) REVERT: A 259 LYS cc_start: 0.8938 (tppt) cc_final: 0.8480 (tppp) REVERT: A 329 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: A 642 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.7017 (m-80) REVERT: A 828 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8419 (m-30) REVERT: A 908 LYS cc_start: 0.8468 (tmmt) cc_final: 0.8256 (tmmt) REVERT: B 23 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7617 (mtp180) REVERT: B 107 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6747 (tm-30) REVERT: B 238 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9058 (mt) REVERT: B 277 GLU cc_start: 0.8062 (tp30) cc_final: 0.7334 (tp30) REVERT: B 319 ASP cc_start: 0.8734 (t70) cc_final: 0.8528 (t0) REVERT: B 881 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: B 893 MET cc_start: 0.7400 (ttp) cc_final: 0.7130 (ttp) REVERT: C 107 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: C 125 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7952 (p0) REVERT: C 245 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8184 (p90) REVERT: C 336 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8211 (mm-30) REVERT: C 472 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8120 (ptp-170) REVERT: C 652 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8003 (tm-30) REVERT: C 705 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7973 (tm) REVERT: C 753 MET cc_start: 0.7930 (tmm) cc_final: 0.7588 (tmm) REVERT: C 863 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8437 (pp20) REVERT: D 14 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7398 (mp0) REVERT: D 115 MET cc_start: 0.7067 (mtp) cc_final: 0.6591 (ttm) REVERT: D 126 MET cc_start: 0.7955 (mtp) cc_final: 0.7713 (mtm) REVERT: D 333 LYS cc_start: 0.7799 (mttt) cc_final: 0.7525 (mmmt) REVERT: D 728 GLN cc_start: 0.7290 (mt0) cc_final: 0.7030 (mm-40) REVERT: D 1016 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8204 (tm-30) outliers start: 104 outliers final: 47 residues processed: 281 average time/residue: 1.5815 time to fit residues: 537.7901 Evaluate side-chains 227 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 167 time to evaluate : 4.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain B residue 878 PHE Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 719 MET Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 905 TYR Chi-restraints excluded: chain D residue 931 LYS Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 993 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 250 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 257 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 318 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 GLN ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38702 Z= 0.182 Angle : 0.524 12.422 53243 Z= 0.277 Chirality : 0.038 0.180 5739 Planarity : 0.004 0.048 6185 Dihedral : 22.439 178.608 6934 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 2.55 % Allowed : 26.58 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.13 (0.13), residues: 4029 helix: 1.14 (0.12), residues: 1938 sheet: -0.21 (0.24), residues: 434 loop : -1.07 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 607 HIS 0.007 0.001 HIS D 850 PHE 0.028 0.001 PHE A 849 TYR 0.028 0.001 TYR D 666 ARG 0.009 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 176 time to evaluate : 4.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7255 (tm-30) cc_final: 0.7039 (tm-30) REVERT: A 126 MET cc_start: 0.8828 (mtp) cc_final: 0.8587 (mtm) REVERT: A 128 ASP cc_start: 0.7922 (t0) cc_final: 0.7664 (t0) REVERT: A 224 ASP cc_start: 0.7640 (t0) cc_final: 0.7370 (t0) REVERT: A 259 LYS cc_start: 0.8956 (tppt) cc_final: 0.8494 (tppp) REVERT: A 329 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7477 (tm-30) REVERT: A 642 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.7034 (m-80) REVERT: A 828 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8440 (m-30) REVERT: A 908 LYS cc_start: 0.8479 (tmmt) cc_final: 0.8270 (tmmt) REVERT: B 23 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7618 (mtp180) REVERT: B 107 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6675 (tm-30) REVERT: B 277 GLU cc_start: 0.8137 (tp30) cc_final: 0.7282 (tp30) REVERT: B 319 ASP cc_start: 0.8716 (t70) cc_final: 0.8501 (t0) REVERT: B 881 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: B 893 MET cc_start: 0.7500 (ttp) cc_final: 0.7270 (ttp) REVERT: C 107 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: C 125 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7936 (p0) REVERT: C 245 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8205 (p90) REVERT: C 336 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8223 (mm-30) REVERT: C 472 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8142 (ptp-170) REVERT: C 652 GLN cc_start: 0.8326 (mm110) cc_final: 0.7919 (tm-30) REVERT: C 705 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7979 (tm) REVERT: C 753 MET cc_start: 0.7819 (tmm) cc_final: 0.7512 (tmm) REVERT: C 863 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8485 (pp20) REVERT: D 14 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7428 (mp0) REVERT: D 59 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7811 (p0) REVERT: D 115 MET cc_start: 0.7092 (mtp) cc_final: 0.6650 (ttm) REVERT: D 126 MET cc_start: 0.8008 (mtp) cc_final: 0.7780 (mtm) REVERT: D 333 LYS cc_start: 0.7754 (mttt) cc_final: 0.7463 (mmmt) REVERT: D 728 GLN cc_start: 0.7285 (mt0) cc_final: 0.7025 (mm-40) REVERT: D 1016 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8200 (tm-30) outliers start: 88 outliers final: 56 residues processed: 248 average time/residue: 1.5735 time to fit residues: 474.1588 Evaluate side-chains 236 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 167 time to evaluate : 3.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 828 ASP Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 719 MET Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 809 GLN Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 905 TYR Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 993 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 368 optimal weight: 10.0000 chunk 387 optimal weight: 0.5980 chunk 353 optimal weight: 1.9990 chunk 377 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 296 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 340 optimal weight: 0.8980 chunk 356 optimal weight: 5.9990 chunk 375 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN ** D 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 ASN D 430 ASN ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 ASN ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 38702 Z= 0.260 Angle : 0.554 12.605 53243 Z= 0.293 Chirality : 0.040 0.175 5739 Planarity : 0.004 0.047 6185 Dihedral : 22.525 178.629 6934 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.57 % Favored : 96.40 % Rotamer: Outliers : 2.55 % Allowed : 26.73 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.10 (0.13), residues: 4029 helix: 1.10 (0.12), residues: 1936 sheet: -0.13 (0.25), residues: 424 loop : -1.08 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 607 HIS 0.004 0.001 HIS D 850 PHE 0.026 0.001 PHE A 849 TYR 0.020 0.001 TYR D 181 ARG 0.009 0.000 ARG A 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 173 time to evaluate : 4.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6986 (tm-30) REVERT: A 128 ASP cc_start: 0.7938 (t0) cc_final: 0.7694 (t0) REVERT: A 224 ASP cc_start: 0.7654 (t0) cc_final: 0.7377 (t0) REVERT: A 259 LYS cc_start: 0.9010 (tppt) cc_final: 0.8575 (tppp) REVERT: A 329 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: A 642 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.7012 (m-80) REVERT: A 828 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8430 (m-30) REVERT: A 908 LYS cc_start: 0.8492 (tmmt) cc_final: 0.8274 (tmmt) REVERT: B 23 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7615 (mtp180) REVERT: B 107 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6711 (tm-30) REVERT: B 277 GLU cc_start: 0.8204 (tp30) cc_final: 0.7307 (tp30) REVERT: B 319 ASP cc_start: 0.8733 (t70) cc_final: 0.8533 (t0) REVERT: B 881 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: C 107 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7410 (tm-30) REVERT: C 245 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8346 (p90) REVERT: C 336 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8267 (mm-30) REVERT: C 472 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8116 (ptp-170) REVERT: C 652 GLN cc_start: 0.8311 (mm110) cc_final: 0.7864 (tm-30) REVERT: C 753 MET cc_start: 0.7880 (tmm) cc_final: 0.7587 (tmm) REVERT: D 14 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7407 (mp0) REVERT: D 115 MET cc_start: 0.7170 (mtp) cc_final: 0.6670 (ttm) REVERT: D 333 LYS cc_start: 0.7749 (mttt) cc_final: 0.7318 (mppt) REVERT: D 728 GLN cc_start: 0.7216 (mt0) cc_final: 0.6968 (mm-40) REVERT: D 905 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.6457 (m-80) REVERT: D 1016 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8231 (tm-30) REVERT: D 1029 MET cc_start: 0.6762 (mpm) cc_final: 0.6534 (mpt) outliers start: 88 outliers final: 56 residues processed: 247 average time/residue: 1.6010 time to fit residues: 477.3476 Evaluate side-chains 234 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 167 time to evaluate : 4.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 719 MET Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 642 PHE Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 809 GLN Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 905 TYR Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 952 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 247 optimal weight: 0.3980 chunk 398 optimal weight: 1.9990 chunk 243 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 277 optimal weight: 3.9990 chunk 418 optimal weight: 10.0000 chunk 385 optimal weight: 7.9990 chunk 333 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 257 optimal weight: 1.9990 chunk 204 optimal weight: 0.0870 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 ASN D 437 GLN D 438 ASN ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38702 Z= 0.185 Angle : 0.532 12.210 53243 Z= 0.281 Chirality : 0.038 0.167 5739 Planarity : 0.004 0.066 6185 Dihedral : 22.391 179.619 6933 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.03 % Allowed : 27.16 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.18 (0.13), residues: 4029 helix: 1.16 (0.12), residues: 1932 sheet: -0.07 (0.25), residues: 428 loop : -1.05 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 639 HIS 0.007 0.001 HIS D 850 PHE 0.026 0.001 PHE A 849 TYR 0.018 0.001 TYR D 181 ARG 0.014 0.000 ARG D 660 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8058 Ramachandran restraints generated. 4029 Oldfield, 0 Emsley, 4029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 184 time to evaluate : 4.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.6885 (mmpt) cc_final: 0.6634 (mmtt) REVERT: A 107 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6859 (tm-30) REVERT: A 126 MET cc_start: 0.8860 (mtp) cc_final: 0.8611 (mtm) REVERT: A 128 ASP cc_start: 0.7974 (t0) cc_final: 0.7722 (t0) REVERT: A 224 ASP cc_start: 0.7638 (t0) cc_final: 0.7357 (t0) REVERT: A 259 LYS cc_start: 0.8984 (tppt) cc_final: 0.8550 (tppp) REVERT: A 329 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: A 642 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.7036 (m-80) REVERT: A 828 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8425 (m-30) REVERT: A 908 LYS cc_start: 0.8494 (tmmt) cc_final: 0.8289 (tmmt) REVERT: B 107 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6666 (tm-30) REVERT: B 277 GLU cc_start: 0.8111 (tp30) cc_final: 0.7302 (tp30) REVERT: B 319 ASP cc_start: 0.8714 (t70) cc_final: 0.8508 (t0) REVERT: B 881 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: C 107 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7413 (tm-30) REVERT: C 336 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8231 (mm-30) REVERT: C 472 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8099 (ptp-170) REVERT: C 652 GLN cc_start: 0.8307 (mm110) cc_final: 0.7903 (tm-30) REVERT: C 705 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7989 (tm) REVERT: C 753 MET cc_start: 0.7890 (tmm) cc_final: 0.7641 (tmm) REVERT: D 14 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7427 (mp0) REVERT: D 115 MET cc_start: 0.7117 (mtp) cc_final: 0.6651 (ttm) REVERT: D 333 LYS cc_start: 0.7814 (mttt) cc_final: 0.7526 (mmmt) REVERT: D 543 MET cc_start: 0.5667 (mmp) cc_final: 0.5427 (mmm) REVERT: D 728 GLN cc_start: 0.7178 (mt0) cc_final: 0.6927 (mm-40) REVERT: D 818 MET cc_start: 0.7436 (mtp) cc_final: 0.7233 (ttm) REVERT: D 905 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6417 (m-80) REVERT: D 1016 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8205 (tm-30) REVERT: D 1029 MET cc_start: 0.6794 (mpm) cc_final: 0.6426 (mpt) outliers start: 70 outliers final: 50 residues processed: 243 average time/residue: 1.6473 time to fit residues: 483.1188 Evaluate side-chains 232 residues out of total 3446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 172 time to evaluate : 4.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 642 PHE Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 472 ARG Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 642 PHE Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 719 MET Chi-restraints excluded: chain C residue 793 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 980 THR Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 642 PHE Chi-restraints excluded: chain D residue 671 VAL Chi-restraints excluded: chain D residue 810 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 905 TYR Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 952 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 264 optimal weight: 0.5980 chunk 354 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 333 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 342 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 ASN ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 ASN ** D 765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.102169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.069844 restraints weight = 79923.795| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.34 r_work: 0.2964 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 38702 Z= 0.167 Angle : 0.532 12.140 53243 Z= 0.280 Chirality : 0.038 0.182 5739 Planarity : 0.004 0.061 6185 Dihedral : 22.293 179.731 6932 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.12 % Allowed : 27.07 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.13), residues: 4029 helix: 1.24 (0.12), residues: 1933 sheet: -0.01 (0.25), residues: 426 loop : -1.00 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 607 HIS 0.007 0.001 HIS D 850 PHE 0.025 0.001 PHE A 849 TYR 0.027 0.001 TYR D 666 ARG 0.015 0.000 ARG D 660 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12771.23 seconds wall clock time: 229 minutes 5.30 seconds (13745.30 seconds total)