Starting phenix.real_space_refine on Wed Feb 21 03:11:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk4_32558/02_2024/7wk4_32558.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk4_32558/02_2024/7wk4_32558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk4_32558/02_2024/7wk4_32558.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk4_32558/02_2024/7wk4_32558.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk4_32558/02_2024/7wk4_32558.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk4_32558/02_2024/7wk4_32558.pdb" } resolution = 3.69 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= 0.006 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 143 5.16 5 C 18904 2.51 5 N 4917 2.21 5 O 5577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D GLU 180": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 661": "OE1" <-> "OE2" Residue "D GLU 702": "OE1" <-> "OE2" Residue "D GLU 725": "OE1" <-> "OE2" Residue "D GLU 748": "OE1" <-> "OE2" Residue "D GLU 773": "OE1" <-> "OE2" Residue "D GLU 780": "OE1" <-> "OE2" Residue "D PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 868": "OE1" <-> "OE2" Residue "D GLU 1017": "OE1" <-> "OE2" Residue "D ARG 1091": "NH1" <-> "NH2" Residue "D ASP 1127": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29541 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4736 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 27, 'TRANS': 553} Chain: "B" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "C" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 54, 'TRANS': 1002} Chain breaks: 7 Chain: "D" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 54, 'TRANS': 1002} Chain breaks: 7 Time building chain proxies: 14.06, per 1000 atoms: 0.48 Number of scatterers: 29541 At special positions: 0 Unit cell: (151.927, 138.811, 233.902, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 143 16.00 O 5577 8.00 N 4917 7.00 C 18904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.04 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.04 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.04 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.33 Conformation dependent library (CDL) restraints added in 5.1 seconds 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7034 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 47 sheets defined 25.7% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.658A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.835A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.525A pdb=" N GLN A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.863A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.646A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 149 removed outlier: 4.069A pdb=" N ASN A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 172 removed outlier: 3.519A pdb=" N TRP A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 removed outlier: 3.596A pdb=" N LEU A 179 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 193 removed outlier: 3.804A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 4.077A pdb=" N TRP A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 204' Processing helix chain 'A' and resid 220 through 248 removed outlier: 4.246A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.658A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 299 removed outlier: 3.977A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 311 removed outlier: 3.797A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 removed outlier: 3.503A pdb=" N VAL A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 382 removed outlier: 3.822A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.524A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.545A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.000A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.572A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 440 removed outlier: 4.155A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.512A pdb=" N MET A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.968A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.805A pdb=" N ILE A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.697A pdb=" N SER A 502 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 503 " --> pdb=" O PRO A 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 499 through 503' Processing helix chain 'A' and resid 515 through 530 removed outlier: 4.134A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N CYS A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.948A pdb=" N GLN A 552 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.645A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.719A pdb=" N LYS B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.804A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 390' Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.719A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.524A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 752 removed outlier: 3.945A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 782 removed outlier: 3.517A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.720A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.533A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.511A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.607A pdb=" N ALA B 924 " --> pdb=" O GLN B 920 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.667A pdb=" N ASP B 950 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.762A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.843A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.556A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.510A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 removed outlier: 3.516A pdb=" N HIS C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 505' Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.649A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.604A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 746 through 751' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.530A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.619A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.541A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.537A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.576A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.648A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.679A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 984 removed outlier: 3.740A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.832A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C1009 " --> pdb=" O GLN C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.892A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.907A pdb=" N LYS D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 417 through 422 removed outlier: 3.959A pdb=" N TYR D 421 " --> pdb=" O ASN D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 639 removed outlier: 3.977A pdb=" N SER D 637 " --> pdb=" O ARG D 634 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR D 638 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY D 639 " --> pdb=" O TYR D 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 634 through 639' Processing helix chain 'D' and resid 737 through 742 removed outlier: 3.533A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 751 removed outlier: 3.966A pdb=" N SER D 750 " --> pdb=" O SER D 746 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN D 751 " --> pdb=" O THR D 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 746 through 751' Processing helix chain 'D' and resid 759 through 770 removed outlier: 3.688A pdb=" N LEU D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 767 " --> pdb=" O LEU D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 783 removed outlier: 3.909A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE D 782 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 824 removed outlier: 4.095A pdb=" N ASN D 824 " --> pdb=" O ASP D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 884 removed outlier: 3.637A pdb=" N THR D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 882 " --> pdb=" O LEU D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 removed outlier: 3.720A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 918 removed outlier: 3.925A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU D 918 " --> pdb=" O ASN D 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 913 through 918' Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.739A pdb=" N THR D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 4.120A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 959 " --> pdb=" O ASN D 955 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN D 965 " --> pdb=" O THR D 961 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 982 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 3.937A pdb=" N GLU D 990 " --> pdb=" O PRO D 986 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE D 993 " --> pdb=" O ALA D 989 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP D 994 " --> pdb=" O GLU D 990 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D1033 " --> pdb=" O MET D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.689A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 3.804A pdb=" N THR A 347 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 359 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 357 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 351 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 23 removed outlier: 5.577A pdb=" N THR B 22 " --> pdb=" O PHE B 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.704A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.658A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.662A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.662A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.444A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.549A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.724A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 400 through 402 removed outlier: 3.659A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.637A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.123A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.412A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.206A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.816A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.882A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.886A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AC4, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.596A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.979A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.998A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 361 through 362 removed outlier: 5.444A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'C' and resid 654 through 660 removed outlier: 3.689A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.845A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.845A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.231A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.469A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 28 through 30 removed outlier: 3.692A pdb=" N VAL D 193 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D 204 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.539A pdb=" N HIS D 49 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 51 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 273 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.912A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY D 107 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 244 through 245 Processing sheet with id=AE1, first strand: chain 'D' and resid 311 through 317 removed outlier: 3.735A pdb=" N THR D 599 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 313 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 325 through 328 removed outlier: 3.620A pdb=" N GLY D 550 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY D 548 " --> pdb=" O PHE D 541 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.593A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL D 511 " --> pdb=" O ILE D 434 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE D 434 " --> pdb=" O VAL D 511 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.617A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.520A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'D' and resid 654 through 660 removed outlier: 4.959A pdb=" N THR D 696 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN D 658 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 666 " --> pdb=" O ILE D 670 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE D 664 " --> pdb=" O ALA D 672 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 712 through 728 removed outlier: 6.664A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASN D 717 " --> pdb=" O ALA D1070 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY D1059 " --> pdb=" O ALA D1056 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.469A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.604A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D1081 " --> pdb=" O HIS D1088 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1094 through 1097 removed outlier: 3.632A pdb=" N VAL D1104 " --> pdb=" O GLN D1113 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.90 Time building geometry restraints manager: 12.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 5779 1.33 - 1.46: 10962 1.46 - 1.60: 13319 1.60 - 1.73: 0 1.73 - 1.86: 194 Bond restraints: 30254 Sorted by residual: bond pdb=" CA THR C 581 " pdb=" C THR C 581 " ideal model delta sigma weight residual 1.533 1.466 0.068 5.60e-03 3.19e+04 1.45e+02 bond pdb=" CA ALA B 989 " pdb=" C ALA B 989 " ideal model delta sigma weight residual 1.524 1.415 0.109 1.27e-02 6.20e+03 7.32e+01 bond pdb=" CA TYR D 380 " pdb=" C TYR D 380 " ideal model delta sigma weight residual 1.523 1.428 0.096 1.34e-02 5.57e+03 5.08e+01 bond pdb=" N ILE C 584 " pdb=" CA ILE C 584 " ideal model delta sigma weight residual 1.459 1.379 0.080 1.15e-02 7.56e+03 4.82e+01 bond pdb=" N ILE D 980 " pdb=" CA ILE D 980 " ideal model delta sigma weight residual 1.461 1.386 0.075 1.17e-02 7.31e+03 4.10e+01 ... (remaining 30249 not shown) Histogram of bond angle deviations from ideal: 99.38 - 107.01: 938 107.01 - 114.64: 17264 114.64 - 122.27: 17698 122.27 - 129.90: 5082 129.90 - 137.52: 152 Bond angle restraints: 41134 Sorted by residual: angle pdb=" CA ASP C 578 " pdb=" C ASP C 578 " pdb=" N PRO C 579 " ideal model delta sigma weight residual 119.27 110.11 9.16 1.13e+00 7.83e-01 6.57e+01 angle pdb=" N ALA B 989 " pdb=" CA ALA B 989 " pdb=" C ALA B 989 " ideal model delta sigma weight residual 111.07 102.61 8.46 1.07e+00 8.73e-01 6.24e+01 angle pdb=" C THR C 581 " pdb=" CA THR C 581 " pdb=" CB THR C 581 " ideal model delta sigma weight residual 117.07 106.24 10.83 1.44e+00 4.82e-01 5.65e+01 angle pdb=" N ILE D 980 " pdb=" CA ILE D 980 " pdb=" C ILE D 980 " ideal model delta sigma weight residual 110.42 103.77 6.65 9.60e-01 1.09e+00 4.80e+01 angle pdb=" N PHE D 981 " pdb=" CA PHE D 981 " pdb=" C PHE D 981 " ideal model delta sigma weight residual 111.28 118.78 -7.50 1.09e+00 8.42e-01 4.74e+01 ... (remaining 41129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16048 17.95 - 35.91: 1586 35.91 - 53.86: 306 53.86 - 71.81: 69 71.81 - 89.77: 26 Dihedral angle restraints: 18035 sinusoidal: 7115 harmonic: 10920 Sorted by residual: dihedral pdb=" CB CYS D 662 " pdb=" SG CYS D 662 " pdb=" SG CYS D 671 " pdb=" CB CYS D 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.42 -80.58 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS D 538 " pdb=" SG CYS D 538 " pdb=" SG CYS D 590 " pdb=" CB CYS D 590 " ideal model delta sinusoidal sigma weight residual 93.00 169.16 -76.16 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -20.80 -65.20 1 1.00e+01 1.00e-02 5.57e+01 ... (remaining 18032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4077 0.088 - 0.176: 452 0.176 - 0.264: 55 0.264 - 0.351: 9 0.351 - 0.439: 1 Chirality restraints: 4594 Sorted by residual: chirality pdb=" CA PHE D 981 " pdb=" N PHE D 981 " pdb=" C PHE D 981 " pdb=" CB PHE D 981 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CA SER D 982 " pdb=" N SER D 982 " pdb=" C SER D 982 " pdb=" CB SER D 982 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA GLU B 990 " pdb=" N GLU B 990 " pdb=" C GLU B 990 " pdb=" CB GLU B 990 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 4591 not shown) Planarity restraints: 5319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 578 " -0.027 2.00e-02 2.50e+03 5.84e-02 3.41e+01 pdb=" C ASP C 578 " 0.101 2.00e-02 2.50e+03 pdb=" O ASP C 578 " -0.040 2.00e-02 2.50e+03 pdb=" N PRO C 579 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 986 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO D 987 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO D 987 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 987 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.066 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO C 987 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.056 5.00e-02 4.00e+02 ... (remaining 5316 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 10080 2.85 - 3.36: 22721 3.36 - 3.88: 48642 3.88 - 4.39: 52644 4.39 - 4.90: 91942 Nonbonded interactions: 226029 Sorted by model distance: nonbonded pdb=" O GLN B 957 " pdb=" OG1 THR B 961 " model vdw 2.338 2.440 nonbonded pdb=" O LEU A 156 " pdb=" OH TYR A 252 " model vdw 2.341 2.440 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.352 2.440 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.356 2.440 nonbonded pdb=" O ASP D 290 " pdb=" OG SER D 297 " model vdw 2.357 2.440 ... (remaining 226024 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 'B' selection = (chain 'C' and (resid 14 through 631 or resid 641 through 1147)) selection = (chain 'D' and (resid 14 through 631 or resid 641 through 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 10.660 Check model and map are aligned: 0.460 Set scattering table: 0.300 Process input model: 77.060 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.140 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 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 : 0.005 0.109 30254 Z= 0.332 Angle : 0.860 12.523 41134 Z= 0.514 Chirality : 0.055 0.439 4594 Planarity : 0.007 0.109 5319 Dihedral : 14.662 89.768 10875 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.40 % Rotamer: Outliers : 0.49 % Allowed : 8.50 % Favored : 91.01 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.10), residues: 3693 helix: -5.04 (0.04), residues: 853 sheet: -1.22 (0.18), residues: 641 loop : -2.49 (0.10), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 275 HIS 0.005 0.001 HIS A 378 PHE 0.034 0.001 PHE B 377 TYR 0.021 0.001 TYR A 385 ARG 0.003 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 605 time to evaluate : 4.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: -0.0669 (tmm) cc_final: -0.0909 (tmm) REVERT: A 383 MET cc_start: 0.3120 (mtp) cc_final: 0.2344 (tpp) REVERT: B 40 ASP cc_start: 0.8699 (p0) cc_final: 0.8476 (p0) REVERT: B 201 PHE cc_start: 0.6278 (m-80) cc_final: 0.6012 (m-80) REVERT: B 308 VAL cc_start: 0.8421 (t) cc_final: 0.8100 (t) REVERT: B 921 LYS cc_start: 0.7127 (mmtp) cc_final: 0.6920 (tttp) REVERT: B 970 PHE cc_start: 0.8374 (m-80) cc_final: 0.7810 (m-80) REVERT: B 1139 ASP cc_start: 0.7026 (t0) cc_final: 0.6727 (p0) REVERT: C 351 TYR cc_start: 0.7649 (p90) cc_final: 0.7311 (p90) REVERT: C 377 PHE cc_start: 0.4885 (p90) cc_final: 0.4310 (p90) REVERT: C 740 MET cc_start: 0.7370 (tpt) cc_final: 0.6989 (tpp) REVERT: D 153 MET cc_start: -0.2134 (ttp) cc_final: -0.2865 (mtm) REVERT: D 436 TRP cc_start: 0.3595 (t60) cc_final: 0.3126 (t-100) REVERT: D 452 LEU cc_start: 0.5650 (mt) cc_final: 0.5320 (mt) REVERT: D 710 ASN cc_start: 0.6396 (p0) cc_final: 0.6146 (p0) REVERT: D 752 LEU cc_start: 0.7923 (mt) cc_final: 0.7670 (mp) REVERT: D 898 PHE cc_start: 0.5868 (m-10) cc_final: 0.5592 (m-80) REVERT: D 950 ASP cc_start: 0.6489 (p0) cc_final: 0.6184 (p0) outliers start: 16 outliers final: 6 residues processed: 619 average time/residue: 0.4198 time to fit residues: 413.7207 Evaluate side-chains 376 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 370 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 407 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 8.9990 chunk 281 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 291 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 337 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 241 HIS ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN B 437 ASN B 542 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B 949 GLN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 134 GLN C 394 ASN C 409 GLN C 448 ASN C 505 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C 935 GLN C 955 ASN C 960 ASN C1054 GLN C1108 ASN C1113 GLN D 61 ASN D 66 HIS D 239 GLN D 394 ASN D 690 GLN ** D 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 ASN D 784 GLN D 901 GLN D 914 ASN D 925 ASN D 926 GLN D 935 GLN D 957 GLN D1010 GLN ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 30254 Z= 0.312 Angle : 0.671 11.407 41134 Z= 0.354 Chirality : 0.045 0.195 4594 Planarity : 0.006 0.073 5319 Dihedral : 4.631 57.618 4023 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.80 % Allowed : 16.48 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.11), residues: 3693 helix: -2.89 (0.12), residues: 905 sheet: -0.58 (0.19), residues: 628 loop : -2.04 (0.11), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 886 HIS 0.009 0.001 HIS C 49 PHE 0.026 0.002 PHE B 643 TYR 0.036 0.002 TYR D 380 ARG 0.007 0.001 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 367 time to evaluate : 3.343 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 190 MET cc_start: -0.0148 (tmm) cc_final: -0.0474 (tmm) REVERT: A 245 ARG cc_start: 0.1099 (ttm170) cc_final: 0.0700 (ttm170) REVERT: A 478 TRP cc_start: 0.3243 (p-90) cc_final: 0.2170 (p-90) REVERT: B 988 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7722 (mp0) REVERT: B 1088 HIS cc_start: 0.6379 (OUTLIER) cc_final: 0.5760 (t-90) REVERT: B 1139 ASP cc_start: 0.6834 (t0) cc_final: 0.6397 (p0) REVERT: C 646 ARG cc_start: 0.6500 (tpt90) cc_final: 0.6289 (tpt170) REVERT: C 725 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8008 (tm-30) REVERT: C 740 MET cc_start: 0.7871 (tpt) cc_final: 0.7228 (tpp) REVERT: C 1050 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6643 (ptp) REVERT: D 90 VAL cc_start: 0.8682 (t) cc_final: 0.8457 (m) REVERT: D 153 MET cc_start: -0.1613 (ttp) cc_final: -0.2646 (mtm) REVERT: D 202 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8395 (tptt) REVERT: D 203 ILE cc_start: 0.8688 (mp) cc_final: 0.8076 (mp) REVERT: D 298 GLU cc_start: 0.6377 (mt-10) cc_final: 0.6144 (mt-10) REVERT: D 436 TRP cc_start: 0.3446 (t60) cc_final: 0.3182 (t-100) REVERT: D 710 ASN cc_start: 0.6838 (p0) cc_final: 0.6444 (p0) REVERT: D 914 ASN cc_start: 0.6868 (m-40) cc_final: 0.6522 (m-40) REVERT: D 965 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7535 (tp-100) outliers start: 92 outliers final: 59 residues processed: 418 average time/residue: 0.4916 time to fit residues: 340.1852 Evaluate side-chains 361 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 300 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 935 GLN Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 1049 LEU Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 281 optimal weight: 7.9990 chunk 230 optimal weight: 0.0980 chunk 93 optimal weight: 7.9990 chunk 338 optimal weight: 1.9990 chunk 365 optimal weight: 6.9990 chunk 301 optimal weight: 0.3980 chunk 335 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 271 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 245 HIS B 271 GLN B 414 GLN B 536 ASN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 717 ASN C 784 GLN C 957 GLN C1002 GLN D 935 GLN D 955 ASN D1005 GLN D1135 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 30254 Z= 0.278 Angle : 0.623 12.076 41134 Z= 0.325 Chirality : 0.045 0.216 4594 Planarity : 0.004 0.060 5319 Dihedral : 4.638 53.351 4022 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.63 % Allowed : 18.46 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.11 (0.12), residues: 3693 helix: -1.09 (0.16), residues: 876 sheet: -0.40 (0.19), residues: 592 loop : -1.88 (0.11), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 886 HIS 0.017 0.001 HIS C 505 PHE 0.029 0.002 PHE C1121 TYR 0.018 0.002 TYR B 707 ARG 0.005 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 326 time to evaluate : 3.143 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: A 190 MET cc_start: -0.0168 (tmm) cc_final: -0.0479 (tmm) REVERT: A 245 ARG cc_start: 0.1061 (ttm170) cc_final: 0.0787 (ttm170) REVERT: A 266 LEU cc_start: -0.0047 (OUTLIER) cc_final: -0.0418 (pp) REVERT: A 297 MET cc_start: -0.2658 (ptm) cc_final: -0.2868 (ptm) REVERT: A 302 TRP cc_start: 0.2211 (OUTLIER) cc_final: -0.0487 (m100) REVERT: A 364 VAL cc_start: 0.3576 (t) cc_final: 0.3371 (m) REVERT: B 301 CYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7463 (t) REVERT: B 552 LEU cc_start: 0.8163 (mt) cc_final: 0.7892 (mp) REVERT: B 725 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7501 (tm-30) REVERT: B 935 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7563 (tp40) REVERT: B 1111 GLU cc_start: 0.6857 (mp0) cc_final: 0.6187 (mp0) REVERT: B 1139 ASP cc_start: 0.6823 (t0) cc_final: 0.6425 (p0) REVERT: C 351 TYR cc_start: 0.7889 (p90) cc_final: 0.7456 (p90) REVERT: C 452 LEU cc_start: 0.8599 (tp) cc_final: 0.7997 (tp) REVERT: C 480 CYS cc_start: 0.0787 (OUTLIER) cc_final: -0.0178 (t) REVERT: C 725 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7729 (tm-30) REVERT: C 740 MET cc_start: 0.8074 (tpt) cc_final: 0.7582 (tpp) REVERT: C 776 LYS cc_start: 0.9027 (tppt) cc_final: 0.8655 (tppp) REVERT: C 1050 MET cc_start: 0.6898 (ptp) cc_final: 0.6352 (ptp) REVERT: D 90 VAL cc_start: 0.8876 (t) cc_final: 0.8608 (m) REVERT: D 153 MET cc_start: -0.1694 (ttp) cc_final: -0.2518 (mtm) REVERT: D 202 LYS cc_start: 0.8639 (ttpt) cc_final: 0.8319 (tptt) REVERT: D 351 TYR cc_start: 0.6407 (p90) cc_final: 0.6049 (p90) REVERT: D 436 TRP cc_start: 0.3887 (t60) cc_final: 0.3626 (t-100) REVERT: D 452 LEU cc_start: 0.5805 (mt) cc_final: 0.5470 (tt) REVERT: D 710 ASN cc_start: 0.7090 (p0) cc_final: 0.6752 (p0) REVERT: D 917 TYR cc_start: 0.7081 (m-80) cc_final: 0.6805 (m-80) REVERT: D 965 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7601 (tp-100) REVERT: D 1017 GLU cc_start: 0.7380 (tp30) cc_final: 0.7077 (tp30) outliers start: 119 outliers final: 74 residues processed: 413 average time/residue: 0.3740 time to fit residues: 256.0964 Evaluate side-chains 367 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 289 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 929 SER Chi-restraints excluded: chain D residue 964 LYS Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 227 optimal weight: 0.0000 chunk 339 optimal weight: 1.9990 chunk 359 optimal weight: 0.7980 chunk 177 optimal weight: 0.5980 chunk 321 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 703 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 30254 Z= 0.172 Angle : 0.546 11.450 41134 Z= 0.277 Chirality : 0.043 0.195 4594 Planarity : 0.004 0.055 5319 Dihedral : 4.254 34.120 4020 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.14 % Allowed : 19.71 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.64 (0.13), residues: 3693 helix: -0.32 (0.17), residues: 872 sheet: -0.30 (0.20), residues: 595 loop : -1.70 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 886 HIS 0.009 0.001 HIS C 49 PHE 0.025 0.001 PHE B 817 TYR 0.016 0.001 TYR B 707 ARG 0.004 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 333 time to evaluate : 3.294 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: A 190 MET cc_start: -0.0364 (tmm) cc_final: -0.0671 (tmm) REVERT: A 245 ARG cc_start: 0.1248 (ttm170) cc_final: 0.1046 (ttm170) REVERT: A 266 LEU cc_start: 0.0059 (OUTLIER) cc_final: -0.0155 (pp) REVERT: A 364 VAL cc_start: 0.3472 (t) cc_final: 0.3269 (m) REVERT: B 290 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7421 (p0) REVERT: B 301 CYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7613 (t) REVERT: B 1139 ASP cc_start: 0.6855 (t0) cc_final: 0.6468 (p0) REVERT: C 271 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7104 (tm-30) REVERT: C 480 CYS cc_start: 0.0874 (OUTLIER) cc_final: -0.0178 (t) REVERT: C 725 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7860 (tm-30) REVERT: C 740 MET cc_start: 0.7981 (tpt) cc_final: 0.7574 (tpp) REVERT: C 954 HIS cc_start: 0.6564 (OUTLIER) cc_final: 0.6234 (m-70) REVERT: C 1050 MET cc_start: 0.6879 (ptp) cc_final: 0.6398 (ptp) REVERT: D 90 VAL cc_start: 0.8836 (t) cc_final: 0.8583 (m) REVERT: D 153 MET cc_start: -0.1702 (ttp) cc_final: -0.2537 (mtm) REVERT: D 202 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8300 (tptt) REVERT: D 351 TYR cc_start: 0.6287 (p90) cc_final: 0.5889 (p90) REVERT: D 436 TRP cc_start: 0.3851 (t60) cc_final: 0.3587 (t-100) REVERT: D 452 LEU cc_start: 0.6002 (mt) cc_final: 0.5590 (tt) REVERT: D 501 TYR cc_start: 0.4960 (OUTLIER) cc_final: 0.4231 (m-80) REVERT: D 710 ASN cc_start: 0.7254 (p0) cc_final: 0.6896 (p0) REVERT: D 767 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7301 (mm) REVERT: D 864 LEU cc_start: 0.8468 (tt) cc_final: 0.8123 (tp) REVERT: D 965 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7696 (tp-100) REVERT: D 1017 GLU cc_start: 0.7308 (tp30) cc_final: 0.7045 (tp30) outliers start: 103 outliers final: 71 residues processed: 400 average time/residue: 0.4295 time to fit residues: 286.5091 Evaluate side-chains 376 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 298 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 8.9990 chunk 204 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 267 optimal weight: 0.6980 chunk 148 optimal weight: 0.5980 chunk 306 optimal weight: 8.9990 chunk 248 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 183 optimal weight: 0.0670 chunk 322 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30254 Z= 0.139 Angle : 0.530 11.226 41134 Z= 0.265 Chirality : 0.043 0.189 4594 Planarity : 0.003 0.054 5319 Dihedral : 4.083 34.166 4020 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.29 % Allowed : 20.78 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.40 (0.13), residues: 3693 helix: -0.01 (0.18), residues: 887 sheet: -0.30 (0.19), residues: 620 loop : -1.57 (0.12), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 886 HIS 0.015 0.001 HIS D 519 PHE 0.021 0.001 PHE D 888 TYR 0.025 0.001 TYR D 917 ARG 0.006 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 329 time to evaluate : 3.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ARG cc_start: 0.1250 (ttm170) cc_final: 0.0808 (ttm170) REVERT: A 266 LEU cc_start: 0.0077 (OUTLIER) cc_final: -0.0267 (pp) REVERT: A 297 MET cc_start: -0.2602 (ptm) cc_final: -0.2839 (ptm) REVERT: A 302 TRP cc_start: 0.2044 (OUTLIER) cc_final: -0.0666 (m100) REVERT: B 121 ASN cc_start: 0.1497 (OUTLIER) cc_final: 0.0450 (m-40) REVERT: B 301 CYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7657 (t) REVERT: B 1111 GLU cc_start: 0.7023 (mp0) cc_final: 0.6323 (mp0) REVERT: B 1139 ASP cc_start: 0.6844 (t0) cc_final: 0.6487 (p0) REVERT: C 400 PHE cc_start: 0.3646 (OUTLIER) cc_final: 0.2360 (p90) REVERT: C 480 CYS cc_start: 0.0839 (OUTLIER) cc_final: -0.0221 (t) REVERT: C 725 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7894 (tm-30) REVERT: C 740 MET cc_start: 0.7964 (tpt) cc_final: 0.7761 (tpp) REVERT: C 774 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8310 (mp10) REVERT: C 954 HIS cc_start: 0.6529 (OUTLIER) cc_final: 0.6195 (m-70) REVERT: C 1050 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.6347 (ptp) REVERT: D 90 VAL cc_start: 0.8812 (t) cc_final: 0.8563 (m) REVERT: D 153 MET cc_start: -0.2168 (ttp) cc_final: -0.2825 (mtm) REVERT: D 202 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8356 (tptt) REVERT: D 436 TRP cc_start: 0.3928 (t60) cc_final: 0.3634 (t-100) REVERT: D 501 TYR cc_start: 0.4979 (OUTLIER) cc_final: 0.4244 (m-80) REVERT: D 864 LEU cc_start: 0.8570 (tt) cc_final: 0.8213 (tp) REVERT: D 965 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7672 (tp-100) REVERT: D 1017 GLU cc_start: 0.7410 (tp30) cc_final: 0.7178 (tp30) outliers start: 108 outliers final: 68 residues processed: 405 average time/residue: 0.3883 time to fit residues: 260.7746 Evaluate side-chains 375 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 298 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 805 ILE Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 0.9980 chunk 323 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 359 optimal weight: 0.7980 chunk 298 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 165 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 188 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN D 710 ASN D 955 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 30254 Z= 0.370 Angle : 0.737 16.135 41134 Z= 0.381 Chirality : 0.048 0.223 4594 Planarity : 0.005 0.051 5319 Dihedral : 5.075 36.940 4018 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 5.12 % Allowed : 20.51 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.78 (0.13), residues: 3693 helix: -0.36 (0.17), residues: 900 sheet: -0.59 (0.19), residues: 643 loop : -1.79 (0.12), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 886 HIS 0.007 0.002 HIS D 49 PHE 0.031 0.003 PHE D 898 TYR 0.026 0.003 TYR B 38 ARG 0.007 0.001 ARG D1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 309 time to evaluate : 3.320 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: A 245 ARG cc_start: 0.1199 (ttm170) cc_final: 0.0946 (tpt170) REVERT: A 266 LEU cc_start: 0.0036 (OUTLIER) cc_final: -0.0318 (pp) REVERT: A 297 MET cc_start: -0.2530 (ptm) cc_final: -0.2764 (ptm) REVERT: A 302 TRP cc_start: 0.2365 (OUTLIER) cc_final: -0.0854 (m100) REVERT: B 231 ILE cc_start: 0.7194 (mm) cc_final: 0.6915 (mm) REVERT: B 255 SER cc_start: 0.7086 (m) cc_final: 0.6809 (t) REVERT: B 301 CYS cc_start: 0.8241 (OUTLIER) cc_final: 0.8014 (t) REVERT: B 1139 ASP cc_start: 0.6731 (t0) cc_final: 0.6328 (p0) REVERT: C 351 TYR cc_start: 0.7925 (p90) cc_final: 0.7588 (p90) REVERT: C 400 PHE cc_start: 0.4536 (OUTLIER) cc_final: 0.3289 (p90) REVERT: C 452 LEU cc_start: 0.8588 (tp) cc_final: 0.7887 (tp) REVERT: C 480 CYS cc_start: 0.1540 (OUTLIER) cc_final: 0.0443 (t) REVERT: C 692 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7378 (mt) REVERT: C 954 HIS cc_start: 0.6769 (OUTLIER) cc_final: 0.6376 (m-70) REVERT: C 1050 MET cc_start: 0.6596 (OUTLIER) cc_final: 0.6109 (ptp) REVERT: D 153 MET cc_start: -0.1797 (ttp) cc_final: -0.2656 (mtm) REVERT: D 202 LYS cc_start: 0.8615 (ttpt) cc_final: 0.8236 (tptt) REVERT: D 346 ARG cc_start: 0.5458 (tpm170) cc_final: 0.5223 (tpm170) REVERT: D 436 TRP cc_start: 0.3973 (t60) cc_final: 0.3643 (t-100) REVERT: D 452 LEU cc_start: 0.6223 (mt) cc_final: 0.5835 (tt) REVERT: D 501 TYR cc_start: 0.4989 (OUTLIER) cc_final: 0.4105 (m-80) REVERT: D 569 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7383 (mp) REVERT: D 868 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8102 (mm-30) REVERT: D 965 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8039 (tp-100) REVERT: D 1005 GLN cc_start: 0.8449 (mm110) cc_final: 0.8248 (mm-40) REVERT: D 1017 GLU cc_start: 0.7495 (tp30) cc_final: 0.7205 (tp30) outliers start: 168 outliers final: 115 residues processed: 437 average time/residue: 0.3574 time to fit residues: 259.0558 Evaluate side-chains 403 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 278 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 234 ASN Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 710 ASN Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 805 ILE Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 929 SER Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1082 CYS Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 205 optimal weight: 0.3980 chunk 262 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 302 optimal weight: 8.9990 chunk 200 optimal weight: 3.9990 chunk 358 optimal weight: 0.9990 chunk 224 optimal weight: 0.6980 chunk 218 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS B 115 GLN B 487 ASN ** B 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 925 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30254 Z= 0.161 Angle : 0.573 14.186 41134 Z= 0.286 Chirality : 0.044 0.195 4594 Planarity : 0.004 0.059 5319 Dihedral : 4.415 37.172 4018 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.96 % Allowed : 22.97 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.37 (0.13), residues: 3693 helix: 0.19 (0.18), residues: 888 sheet: -0.52 (0.20), residues: 635 loop : -1.55 (0.12), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 886 HIS 0.007 0.001 HIS C 49 PHE 0.024 0.001 PHE C 157 TYR 0.022 0.001 TYR D 917 ARG 0.005 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 322 time to evaluate : 3.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: 0.0008 (OUTLIER) cc_final: -0.0307 (pp) REVERT: A 302 TRP cc_start: 0.1819 (OUTLIER) cc_final: -0.1111 (m100) REVERT: B 223 LEU cc_start: 0.8760 (mp) cc_final: 0.8415 (mt) REVERT: B 255 SER cc_start: 0.7042 (m) cc_final: 0.6770 (t) REVERT: B 567 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7771 (tpp80) REVERT: B 1139 ASP cc_start: 0.6477 (t0) cc_final: 0.6262 (p0) REVERT: C 400 PHE cc_start: 0.4304 (OUTLIER) cc_final: 0.3022 (p90) REVERT: C 480 CYS cc_start: 0.0700 (OUTLIER) cc_final: -0.0322 (t) REVERT: C 692 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7329 (mt) REVERT: C 765 ARG cc_start: 0.7735 (ttp-170) cc_final: 0.7510 (ttp-170) REVERT: C 954 HIS cc_start: 0.6579 (OUTLIER) cc_final: 0.6239 (m-70) REVERT: C 977 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8063 (mp) REVERT: C 1050 MET cc_start: 0.6529 (ptp) cc_final: 0.6214 (ptp) REVERT: D 153 MET cc_start: -0.2418 (ttp) cc_final: -0.3184 (mtm) REVERT: D 202 LYS cc_start: 0.8628 (ttpt) cc_final: 0.8287 (tptt) REVERT: D 436 TRP cc_start: 0.3885 (t60) cc_final: 0.3576 (t-100) REVERT: D 501 TYR cc_start: 0.5067 (OUTLIER) cc_final: 0.4211 (m-80) REVERT: D 864 LEU cc_start: 0.8578 (tt) cc_final: 0.8216 (tp) REVERT: D 868 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7762 (mm-30) REVERT: D 965 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7967 (tp-100) REVERT: D 1017 GLU cc_start: 0.7418 (tp30) cc_final: 0.7117 (tp30) outliers start: 97 outliers final: 67 residues processed: 393 average time/residue: 0.3768 time to fit residues: 242.8008 Evaluate side-chains 373 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 298 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 805 ILE Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1121 PHE Chi-restraints excluded: chain D residue 1132 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 281 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN D 710 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 30254 Z= 0.306 Angle : 0.665 12.939 41134 Z= 0.340 Chirality : 0.046 0.231 4594 Planarity : 0.005 0.078 5319 Dihedral : 4.771 38.121 4018 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.81 % Allowed : 23.25 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.57 (0.13), residues: 3693 helix: 0.08 (0.18), residues: 883 sheet: -0.65 (0.19), residues: 651 loop : -1.71 (0.12), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 886 HIS 0.028 0.002 HIS A 505 PHE 0.022 0.002 PHE B 888 TYR 0.032 0.002 TYR D1007 ARG 0.014 0.001 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 293 time to evaluate : 3.211 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: A 266 LEU cc_start: -0.0050 (OUTLIER) cc_final: -0.0342 (pp) REVERT: A 302 TRP cc_start: 0.2255 (OUTLIER) cc_final: -0.0852 (m100) REVERT: A 557 MET cc_start: 0.0295 (mmp) cc_final: -0.0558 (tmm) REVERT: B 255 SER cc_start: 0.7010 (m) cc_final: 0.6715 (t) REVERT: B 298 GLU cc_start: 0.8637 (tp30) cc_final: 0.8259 (tp30) REVERT: B 740 MET cc_start: 0.6732 (tpp) cc_final: 0.6258 (tpp) REVERT: B 1139 ASP cc_start: 0.6462 (t0) cc_final: 0.6201 (p0) REVERT: C 351 TYR cc_start: 0.7923 (p90) cc_final: 0.7564 (p90) REVERT: C 400 PHE cc_start: 0.4521 (OUTLIER) cc_final: 0.3120 (p90) REVERT: C 480 CYS cc_start: 0.0623 (OUTLIER) cc_final: -0.0367 (t) REVERT: C 692 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7431 (mt) REVERT: C 765 ARG cc_start: 0.7932 (ttp-170) cc_final: 0.7670 (ttm170) REVERT: C 954 HIS cc_start: 0.6697 (OUTLIER) cc_final: 0.6312 (m-70) REVERT: C 1050 MET cc_start: 0.6658 (ptp) cc_final: 0.6288 (ptm) REVERT: D 153 MET cc_start: -0.2344 (ttp) cc_final: -0.3045 (mtm) REVERT: D 202 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8269 (tptt) REVERT: D 436 TRP cc_start: 0.3888 (t60) cc_final: 0.3605 (t-100) REVERT: D 501 TYR cc_start: 0.5207 (OUTLIER) cc_final: 0.4209 (m-80) REVERT: D 864 LEU cc_start: 0.8663 (tt) cc_final: 0.8244 (tp) REVERT: D 965 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7958 (tp-100) REVERT: D 1017 GLU cc_start: 0.7406 (tp30) cc_final: 0.7180 (tp30) REVERT: D 1050 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7218 (ptp) outliers start: 125 outliers final: 107 residues processed: 382 average time/residue: 0.4002 time to fit residues: 250.7497 Evaluate side-chains 392 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 277 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 710 ASN Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 805 ILE Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1082 CYS Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 0.8980 chunk 343 optimal weight: 0.0020 chunk 313 optimal weight: 6.9990 chunk 334 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 262 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 316 optimal weight: 5.9990 chunk 332 optimal weight: 3.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN D 710 ASN D 953 ASN D 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30254 Z= 0.180 Angle : 0.597 12.650 41134 Z= 0.299 Chirality : 0.045 0.204 4594 Planarity : 0.004 0.050 5319 Dihedral : 4.523 37.735 4018 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.60 % Allowed : 23.83 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.37 (0.13), residues: 3693 helix: 0.29 (0.18), residues: 883 sheet: -0.54 (0.19), residues: 651 loop : -1.60 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 886 HIS 0.009 0.001 HIS B 954 PHE 0.019 0.001 PHE B 375 TYR 0.030 0.001 TYR D1007 ARG 0.008 0.000 ARG D 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 302 time to evaluate : 3.149 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: A 266 LEU cc_start: 0.0190 (OUTLIER) cc_final: -0.0109 (pp) REVERT: A 302 TRP cc_start: 0.2030 (OUTLIER) cc_final: -0.0928 (m100) REVERT: A 557 MET cc_start: 0.0109 (mmp) cc_final: -0.0590 (tmm) REVERT: B 223 LEU cc_start: 0.8777 (mp) cc_final: 0.8455 (mt) REVERT: B 255 SER cc_start: 0.6985 (m) cc_final: 0.6696 (t) REVERT: B 965 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7325 (mm-40) REVERT: B 1139 ASP cc_start: 0.6453 (t0) cc_final: 0.6216 (p0) REVERT: C 351 TYR cc_start: 0.7916 (p90) cc_final: 0.7548 (p90) REVERT: C 400 PHE cc_start: 0.4546 (OUTLIER) cc_final: 0.3060 (p90) REVERT: C 480 CYS cc_start: 0.0474 (OUTLIER) cc_final: -0.0473 (t) REVERT: C 692 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7331 (mt) REVERT: C 765 ARG cc_start: 0.7876 (ttp-170) cc_final: 0.7668 (ttm170) REVERT: C 954 HIS cc_start: 0.6745 (OUTLIER) cc_final: 0.6349 (m-70) REVERT: C 977 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8026 (mp) REVERT: C 1050 MET cc_start: 0.6564 (ptp) cc_final: 0.6253 (ptp) REVERT: D 153 MET cc_start: -0.2230 (ttp) cc_final: -0.2958 (mtm) REVERT: D 202 LYS cc_start: 0.8596 (ttpt) cc_final: 0.8224 (tptt) REVERT: D 436 TRP cc_start: 0.3870 (t60) cc_final: 0.3647 (t-100) REVERT: D 501 TYR cc_start: 0.5207 (OUTLIER) cc_final: 0.4214 (m-80) REVERT: D 864 LEU cc_start: 0.8587 (tt) cc_final: 0.8315 (tp) REVERT: D 965 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7872 (tp-100) REVERT: D 1017 GLU cc_start: 0.7350 (tp30) cc_final: 0.7070 (tp30) REVERT: D 1018 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8865 (tp) REVERT: D 1050 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7281 (ptp) outliers start: 118 outliers final: 92 residues processed: 386 average time/residue: 0.3748 time to fit residues: 239.9750 Evaluate side-chains 389 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 287 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 710 ASN Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 805 ILE Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1018 ILE Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1082 CYS Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 4.9990 chunk 353 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 245 optimal weight: 0.6980 chunk 370 optimal weight: 10.0000 chunk 341 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1002 GLN D 710 ASN D 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.6134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30254 Z= 0.243 Angle : 0.636 11.709 41134 Z= 0.322 Chirality : 0.045 0.207 4594 Planarity : 0.004 0.062 5319 Dihedral : 4.640 37.996 4018 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.53 % Allowed : 24.13 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.46 (0.13), residues: 3693 helix: 0.18 (0.18), residues: 907 sheet: -0.61 (0.19), residues: 660 loop : -1.64 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 886 HIS 0.010 0.001 HIS B 954 PHE 0.021 0.002 PHE B 559 TYR 0.032 0.002 TYR D1007 ARG 0.007 0.001 ARG D 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 292 time to evaluate : 3.628 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: A 266 LEU cc_start: 0.0235 (OUTLIER) cc_final: -0.0073 (pp) REVERT: A 302 TRP cc_start: 0.2067 (OUTLIER) cc_final: -0.0920 (m100) REVERT: A 557 MET cc_start: -0.0046 (mmp) cc_final: -0.0744 (tmm) REVERT: B 223 LEU cc_start: 0.8878 (mp) cc_final: 0.8588 (mt) REVERT: B 255 SER cc_start: 0.7001 (m) cc_final: 0.6710 (t) REVERT: B 740 MET cc_start: 0.6695 (tpp) cc_final: 0.6215 (tpp) REVERT: B 984 LEU cc_start: 0.8588 (mp) cc_final: 0.8366 (mp) REVERT: B 1139 ASP cc_start: 0.6380 (t0) cc_final: 0.6080 (p0) REVERT: C 351 TYR cc_start: 0.7954 (p90) cc_final: 0.7593 (p90) REVERT: C 357 ARG cc_start: 0.8639 (tpp-160) cc_final: 0.8246 (tpp-160) REVERT: C 400 PHE cc_start: 0.4465 (OUTLIER) cc_final: 0.2925 (p90) REVERT: C 480 CYS cc_start: 0.0769 (OUTLIER) cc_final: -0.0160 (t) REVERT: C 634 ARG cc_start: 0.1373 (OUTLIER) cc_final: 0.1164 (tpt-90) REVERT: C 692 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7344 (mt) REVERT: C 740 MET cc_start: 0.7432 (tpp) cc_final: 0.7208 (tpt) REVERT: C 765 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7715 (ttm170) REVERT: C 954 HIS cc_start: 0.6689 (OUTLIER) cc_final: 0.6312 (m-70) REVERT: C 1050 MET cc_start: 0.6618 (ptp) cc_final: 0.6268 (ptm) REVERT: D 153 MET cc_start: -0.2365 (ttp) cc_final: -0.3261 (mtm) REVERT: D 202 LYS cc_start: 0.8644 (ttpt) cc_final: 0.8234 (tptt) REVERT: D 436 TRP cc_start: 0.3896 (t60) cc_final: 0.3669 (t-100) REVERT: D 501 TYR cc_start: 0.5189 (OUTLIER) cc_final: 0.4172 (m-80) REVERT: D 864 LEU cc_start: 0.8628 (tt) cc_final: 0.8208 (tp) REVERT: D 965 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7901 (tp-100) REVERT: D 1017 GLU cc_start: 0.7393 (tp30) cc_final: 0.7125 (tp30) outliers start: 116 outliers final: 102 residues processed: 372 average time/residue: 0.3794 time to fit residues: 233.4436 Evaluate side-chains 391 residues out of total 3282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 281 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 571 GLU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 477 ASN Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 417 ASN Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 752 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 805 ILE Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1082 CYS Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 0.4980 chunk 314 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 295 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 303 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 0.0870 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 953 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.140974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.113010 restraints weight = 114315.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.113443 restraints weight = 84792.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.113890 restraints weight = 53790.397| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30254 Z= 0.168 Angle : 0.589 12.081 41134 Z= 0.295 Chirality : 0.044 0.201 4594 Planarity : 0.004 0.060 5319 Dihedral : 4.414 38.716 4018 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.20 % Allowed : 24.59 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 3693 helix: 0.50 (0.18), residues: 878 sheet: -0.49 (0.20), residues: 633 loop : -1.56 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 886 HIS 0.009 0.001 HIS B 954 PHE 0.025 0.001 PHE D 981 TYR 0.025 0.001 TYR D1007 ARG 0.005 0.000 ARG D 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6254.91 seconds wall clock time: 114 minutes 40.57 seconds (6880.57 seconds total)