Starting phenix.real_space_refine on Mon Mar 18 08:00:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/03_2024/8t1d_40960_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/03_2024/8t1d_40960.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/03_2024/8t1d_40960_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/03_2024/8t1d_40960_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/03_2024/8t1d_40960_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/03_2024/8t1d_40960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/03_2024/8t1d_40960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/03_2024/8t1d_40960_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/03_2024/8t1d_40960_updated.pdb" } resolution = 3.35 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= 0.001 sd= 0.010 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 104 5.16 5 C 13268 2.51 5 N 3344 2.21 5 O 3622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 160": "NH1" <-> "NH2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A ARG 757": "NH1" <-> "NH2" Residue "A ARG 779": "NH1" <-> "NH2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 616": "NH1" <-> "NH2" Residue "B ARG 661": "NH1" <-> "NH2" Residue "B ARG 746": "NH1" <-> "NH2" Residue "B ARG 757": "NH1" <-> "NH2" Residue "B ARG 779": "NH1" <-> "NH2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 391": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 616": "NH1" <-> "NH2" Residue "C ARG 661": "NH1" <-> "NH2" Residue "C ARG 746": "NH1" <-> "NH2" Residue "C ARG 757": "NH1" <-> "NH2" Residue "C ARG 779": "NH1" <-> "NH2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D ARG 271": "NH1" <-> "NH2" Residue "D ARG 391": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 616": "NH1" <-> "NH2" Residue "D ARG 661": "NH1" <-> "NH2" Residue "D ARG 746": "NH1" <-> "NH2" Residue "D ARG 757": "NH1" <-> "NH2" Residue "D ARG 779": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20338 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 5086 Classifications: {'peptide': 632} Link IDs: {'PTRANS': 25, 'TRANS': 606} Chain breaks: 1 Chain: "B" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4987 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 24, 'TRANS': 594} Chain breaks: 2 Chain: "C" Number of atoms: 5086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 5086 Classifications: {'peptide': 632} Link IDs: {'PTRANS': 25, 'TRANS': 606} Chain breaks: 1 Chain: "D" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4987 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 24, 'TRANS': 594} Chain breaks: 2 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'XS9': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'XS9': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'XS9': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'XS9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.36, per 1000 atoms: 0.51 Number of scatterers: 20338 At special positions: 0 Unit cell: (145.928, 153.816, 124.63, 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 104 16.00 O 3622 8.00 N 3344 7.00 C 13268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 639 " - pdb=" SG CYS A 660 " distance=2.03 Simple disulfide: pdb=" SG CYS B 639 " - pdb=" SG CYS B 660 " distance=2.03 Simple disulfide: pdb=" SG CYS C 639 " - pdb=" SG CYS C 660 " distance=2.03 Simple disulfide: pdb=" SG CYS D 639 " - pdb=" SG CYS D 660 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.77 Conformation dependent library (CDL) restraints added in 3.4 seconds 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 122 helices and 4 sheets defined 53.0% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 151 through 160 removed outlier: 4.157A pdb=" N PHE A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 194 through 200 Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.518A pdb=" N ILE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 removed outlier: 3.910A pdb=" N ILE A 227 " --> pdb=" O MET A 223 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASN A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 228' Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.626A pdb=" N GLU A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 256 " --> pdb=" O HIS A 252 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.566A pdb=" N THR A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 338 through 355 removed outlier: 3.828A pdb=" N THR A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 373 through 379 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.754A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.593A pdb=" N VAL A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 455 through 465 removed outlier: 3.665A pdb=" N LEU A 459 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 460 " --> pdb=" O ASN A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 490 removed outlier: 3.542A pdb=" N VAL A 476 " --> pdb=" O TYR A 472 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 484 " --> pdb=" O CYS A 480 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 523 removed outlier: 3.993A pdb=" N VAL A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.585A pdb=" N ILE A 529 " --> pdb=" O PHE A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 568 removed outlier: 3.924A pdb=" N ILE A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 587 removed outlier: 4.047A pdb=" N LEU A 575 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 576 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 579 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 583 " --> pdb=" O PHE A 580 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 584 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET A 587 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 593 removed outlier: 3.711A pdb=" N THR A 593 " --> pdb=" O LEU A 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 590 through 593' Processing helix chain 'A' and resid 597 through 610 removed outlier: 3.549A pdb=" N SER A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 631 removed outlier: 3.717A pdb=" N VAL A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A 628 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 630 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 674 removed outlier: 3.670A pdb=" N LEU A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 705 removed outlier: 4.433A pdb=" N ILE A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 721 removed outlier: 3.734A pdb=" N GLU A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 747 removed outlier: 3.752A pdb=" N LYS A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 741 " --> pdb=" O TRP A 737 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 756 Processing helix chain 'A' and resid 787 through 790 No H-bonds generated for 'chain 'A' and resid 787 through 790' Processing helix chain 'B' and resid 151 through 160 removed outlier: 3.685A pdb=" N PHE B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.888A pdb=" N VAL B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 227 No H-bonds generated for 'chain 'B' and resid 224 through 227' Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 251 through 259 removed outlier: 3.524A pdb=" N LEU B 256 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 288 through 294 removed outlier: 3.559A pdb=" N ALA B 292 " --> pdb=" O PRO B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.679A pdb=" N VAL B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 355 removed outlier: 4.063A pdb=" N THR B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.634A pdb=" N ALA B 377 " --> pdb=" O PRO B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.855A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 390' Processing helix chain 'B' and resid 433 through 436 No H-bonds generated for 'chain 'B' and resid 433 through 436' Processing helix chain 'B' and resid 446 through 449 No H-bonds generated for 'chain 'B' and resid 446 through 449' Processing helix chain 'B' and resid 454 through 463 removed outlier: 3.688A pdb=" N ARG B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 490 removed outlier: 3.609A pdb=" N ILE B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR B 478 " --> pdb=" O ASN B 474 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 529 removed outlier: 3.560A pdb=" N GLU B 514 " --> pdb=" O ARG B 510 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 568 removed outlier: 3.598A pdb=" N TYR B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 560 " --> pdb=" O TYR B 556 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 568 " --> pdb=" O ALA B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 589 removed outlier: 3.911A pdb=" N LEU B 575 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET B 578 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 579 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL B 583 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY B 585 " --> pdb=" O LEU B 582 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP B 586 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 589 " --> pdb=" O TRP B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 601 Processing helix chain 'B' and resid 605 through 634 removed outlier: 3.753A pdb=" N PHE B 611 " --> pdb=" O GLN B 607 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 612 " --> pdb=" O LYS B 608 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 613 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE B 615 " --> pdb=" O PHE B 611 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL B 620 " --> pdb=" O ARG B 616 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 630 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 678 removed outlier: 4.480A pdb=" N LEU B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 675 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 704 removed outlier: 4.040A pdb=" N ILE B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 727 removed outlier: 4.493A pdb=" N GLY B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN B 724 " --> pdb=" O GLU B 720 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 747 removed outlier: 3.802A pdb=" N TRP B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU B 735 " --> pdb=" O HIS B 731 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 747 " --> pdb=" O ASP B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 755 Processing helix chain 'B' and resid 786 through 790 removed outlier: 4.089A pdb=" N GLN B 790 " --> pdb=" O SER B 786 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 786 through 790' Processing helix chain 'C' and resid 151 through 160 removed outlier: 4.157A pdb=" N PHE C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP C 156 " --> pdb=" O PRO C 152 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 175 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 194 through 200 Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.518A pdb=" N ILE C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 removed outlier: 3.910A pdb=" N ILE C 227 " --> pdb=" O MET C 223 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASN C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 223 through 228' Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'C' and resid 251 through 259 removed outlier: 3.626A pdb=" N GLU C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 256 " --> pdb=" O HIS C 252 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.566A pdb=" N THR C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 338 through 355 removed outlier: 3.828A pdb=" N THR C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 349 " --> pdb=" O MET C 345 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 373 through 379 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.754A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 390 " --> pdb=" O PHE C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 438 removed outlier: 3.594A pdb=" N VAL C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 455 through 465 removed outlier: 3.665A pdb=" N LEU C 459 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 460 " --> pdb=" O ASN C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 490 removed outlier: 3.541A pdb=" N VAL C 476 " --> pdb=" O TYR C 472 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE C 484 " --> pdb=" O CYS C 480 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 523 removed outlier: 3.993A pdb=" N VAL C 515 " --> pdb=" O LEU C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 533 removed outlier: 3.585A pdb=" N ILE C 529 " --> pdb=" O PHE C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 568 removed outlier: 3.924A pdb=" N ILE C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 587 removed outlier: 4.047A pdb=" N LEU C 575 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 576 " --> pdb=" O ALA C 573 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL C 579 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 583 " --> pdb=" O PHE C 580 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU C 584 " --> pdb=" O ALA C 581 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET C 587 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 593 removed outlier: 3.711A pdb=" N THR C 593 " --> pdb=" O LEU C 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 593' Processing helix chain 'C' and resid 597 through 610 removed outlier: 3.548A pdb=" N SER C 603 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 606 " --> pdb=" O TYR C 602 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 607 " --> pdb=" O SER C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 631 removed outlier: 3.716A pdb=" N VAL C 620 " --> pdb=" O ARG C 616 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C 628 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 630 " --> pdb=" O ILE C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 674 removed outlier: 3.670A pdb=" N LEU C 671 " --> pdb=" O SER C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 705 removed outlier: 4.433A pdb=" N ILE C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 721 removed outlier: 3.734A pdb=" N GLU C 720 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 747 removed outlier: 3.752A pdb=" N LYS C 730 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS C 731 " --> pdb=" O LYS C 727 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 741 " --> pdb=" O TRP C 737 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 742 " --> pdb=" O ALA C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 756 Processing helix chain 'C' and resid 787 through 790 No H-bonds generated for 'chain 'C' and resid 787 through 790' Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.686A pdb=" N PHE D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 175 Processing helix chain 'D' and resid 194 through 200 Processing helix chain 'D' and resid 208 through 220 removed outlier: 3.888A pdb=" N VAL D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 227 No H-bonds generated for 'chain 'D' and resid 224 through 227' Processing helix chain 'D' and resid 241 through 247 Processing helix chain 'D' and resid 251 through 259 removed outlier: 3.524A pdb=" N LEU D 256 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 288 through 294 removed outlier: 3.560A pdb=" N ALA D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 324 through 330 removed outlier: 3.680A pdb=" N VAL D 329 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 355 removed outlier: 4.063A pdb=" N THR D 343 " --> pdb=" O THR D 339 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS D 352 " --> pdb=" O LEU D 348 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS D 353 " --> pdb=" O LEU D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 379 removed outlier: 3.634A pdb=" N ALA D 377 " --> pdb=" O PRO D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 390 removed outlier: 3.855A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 389 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 390 " --> pdb=" O PHE D 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 384 through 390' Processing helix chain 'D' and resid 433 through 436 No H-bonds generated for 'chain 'D' and resid 433 through 436' Processing helix chain 'D' and resid 446 through 449 No H-bonds generated for 'chain 'D' and resid 446 through 449' Processing helix chain 'D' and resid 454 through 463 removed outlier: 3.688A pdb=" N ARG D 460 " --> pdb=" O ASN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 490 removed outlier: 3.610A pdb=" N ILE D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR D 478 " --> pdb=" O ASN D 474 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA D 481 " --> pdb=" O SER D 477 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 529 removed outlier: 3.561A pdb=" N GLU D 514 " --> pdb=" O ARG D 510 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL D 515 " --> pdb=" O LEU D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 568 removed outlier: 3.598A pdb=" N TYR D 553 " --> pdb=" O PHE D 549 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 560 " --> pdb=" O TYR D 556 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 568 " --> pdb=" O ALA D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 589 removed outlier: 3.911A pdb=" N LEU D 575 " --> pdb=" O GLU D 572 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET D 578 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL D 579 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL D 583 " --> pdb=" O PHE D 580 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY D 585 " --> pdb=" O LEU D 582 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP D 586 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 589 " --> pdb=" O TRP D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 601 Processing helix chain 'D' and resid 605 through 634 removed outlier: 3.754A pdb=" N PHE D 611 " --> pdb=" O GLN D 607 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS D 612 " --> pdb=" O LYS D 608 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP D 613 " --> pdb=" O ILE D 609 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE D 615 " --> pdb=" O PHE D 611 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL D 620 " --> pdb=" O ARG D 616 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 626 " --> pdb=" O LEU D 622 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY D 627 " --> pdb=" O LEU D 623 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 630 " --> pdb=" O ILE D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 678 removed outlier: 4.479A pdb=" N LEU D 670 " --> pdb=" O PHE D 666 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS D 675 " --> pdb=" O LEU D 671 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 704 removed outlier: 4.040A pdb=" N ILE D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 727 removed outlier: 4.492A pdb=" N GLY D 723 " --> pdb=" O GLY D 719 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN D 724 " --> pdb=" O GLU D 720 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL D 725 " --> pdb=" O THR D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 747 removed outlier: 3.801A pdb=" N TRP D 733 " --> pdb=" O SER D 729 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU D 735 " --> pdb=" O HIS D 731 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 747 " --> pdb=" O ASP D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 755 Processing helix chain 'D' and resid 786 through 790 removed outlier: 4.088A pdb=" N GLN D 790 " --> pdb=" O SER D 786 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 786 through 790' Processing sheet with id= A, first strand: chain 'A' and resid 760 through 763 removed outlier: 3.586A pdb=" N ARG A 775 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP A 409 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU A 418 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LYS A 407 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ASP A 420 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYS A 405 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 418 through 420 Processing sheet with id= C, first strand: chain 'C' and resid 760 through 763 removed outlier: 3.586A pdb=" N ARG C 775 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP C 409 " --> pdb=" O SER C 416 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU C 418 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LYS C 407 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ASP C 420 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LYS C 405 " --> pdb=" O ASP C 420 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 418 through 420 676 hydrogen bonds defined for protein. 1914 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 8.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3328 1.32 - 1.44: 5606 1.44 - 1.57: 11719 1.57 - 1.69: 1 1.69 - 1.81: 170 Bond restraints: 20824 Sorted by residual: bond pdb=" C15 XS9 A1201 " pdb=" C21 XS9 A1201 " ideal model delta sigma weight residual 0.000 1.549 -1.549 2.00e-02 2.50e+03 6.00e+03 bond pdb=" C15 XS9 C1201 " pdb=" C21 XS9 C1201 " ideal model delta sigma weight residual 0.000 1.549 -1.549 2.00e-02 2.50e+03 6.00e+03 bond pdb=" C15 XS9 D1201 " pdb=" C21 XS9 D1201 " ideal model delta sigma weight residual 0.000 1.548 -1.548 2.00e-02 2.50e+03 5.99e+03 bond pdb=" C15 XS9 B1201 " pdb=" C21 XS9 B1201 " ideal model delta sigma weight residual 0.000 1.548 -1.548 2.00e-02 2.50e+03 5.99e+03 bond pdb=" C18 XS9 D1201 " pdb=" C19 XS9 D1201 " ideal model delta sigma weight residual 0.927 1.504 -0.577 2.00e-02 2.50e+03 8.33e+02 ... (remaining 20819 not shown) Histogram of bond angle deviations from ideal: 59.22 - 75.05: 12 75.05 - 90.87: 0 90.87 - 106.70: 629 106.70 - 122.53: 25274 122.53 - 138.35: 2357 Bond angle restraints: 28272 Sorted by residual: angle pdb=" C16 XS9 D1201 " pdb=" C30 XS9 D1201 " pdb=" C32 XS9 D1201 " ideal model delta sigma weight residual 160.11 125.77 34.34 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C16 XS9 B1201 " pdb=" C30 XS9 B1201 " pdb=" C32 XS9 B1201 " ideal model delta sigma weight residual 160.11 125.82 34.29 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C16 XS9 C1201 " pdb=" C30 XS9 C1201 " pdb=" C32 XS9 C1201 " ideal model delta sigma weight residual 160.11 128.80 31.31 3.00e+00 1.11e-01 1.09e+02 angle pdb=" C16 XS9 A1201 " pdb=" C30 XS9 A1201 " pdb=" C32 XS9 A1201 " ideal model delta sigma weight residual 160.11 128.80 31.31 3.00e+00 1.11e-01 1.09e+02 angle pdb=" C SER A 663 " pdb=" N GLU A 664 " pdb=" CA GLU A 664 " ideal model delta sigma weight residual 121.54 136.57 -15.03 1.91e+00 2.74e-01 6.19e+01 ... (remaining 28267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.78: 11832 23.78 - 47.56: 484 47.56 - 71.34: 58 71.34 - 95.11: 6 95.11 - 118.89: 6 Dihedral angle restraints: 12386 sinusoidal: 5050 harmonic: 7336 Sorted by residual: dihedral pdb=" CA GLU C 453 " pdb=" C GLU C 453 " pdb=" N PRO C 454 " pdb=" CA PRO C 454 " ideal model delta harmonic sigma weight residual 180.00 -127.45 -52.55 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA GLU A 453 " pdb=" C GLU A 453 " pdb=" N PRO A 454 " pdb=" CA PRO A 454 " ideal model delta harmonic sigma weight residual -180.00 -127.45 -52.55 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA GLU C 664 " pdb=" C GLU C 664 " pdb=" N THR C 665 " pdb=" CA THR C 665 " ideal model delta harmonic sigma weight residual 180.00 127.88 52.12 0 5.00e+00 4.00e-02 1.09e+02 ... (remaining 12383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.130: 3214 1.130 - 2.260: 0 2.260 - 3.390: 0 3.390 - 4.521: 0 4.521 - 5.651: 4 Chirality restraints: 3218 Sorted by residual: chirality pdb=" C20 XS9 C1201 " pdb=" C19 XS9 C1201 " pdb=" C21 XS9 C1201 " pdb=" C24 XS9 C1201 " both_signs ideal model delta sigma weight residual False -2.81 2.84 -5.65 2.00e-01 2.50e+01 7.98e+02 chirality pdb=" C20 XS9 A1201 " pdb=" C19 XS9 A1201 " pdb=" C21 XS9 A1201 " pdb=" C24 XS9 A1201 " both_signs ideal model delta sigma weight residual False -2.81 2.83 -5.65 2.00e-01 2.50e+01 7.97e+02 chirality pdb=" C20 XS9 B1201 " pdb=" C19 XS9 B1201 " pdb=" C21 XS9 B1201 " pdb=" C24 XS9 B1201 " both_signs ideal model delta sigma weight residual False -2.81 2.72 -5.53 2.00e-01 2.50e+01 7.66e+02 ... (remaining 3215 not shown) Planarity restraints: 3512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 453 " -0.064 5.00e-02 4.00e+02 9.70e-02 1.50e+01 pdb=" N PRO C 454 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO C 454 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 454 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 453 " 0.064 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO A 454 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 454 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 454 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 665 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C THR A 665 " -0.055 2.00e-02 2.50e+03 pdb=" O THR A 665 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE A 666 " 0.019 2.00e-02 2.50e+03 ... (remaining 3509 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1110 2.72 - 3.26: 20380 3.26 - 3.81: 32668 3.81 - 4.35: 41230 4.35 - 4.90: 66811 Nonbonded interactions: 162199 Sorted by model distance: nonbonded pdb=" O TYR D 702 " pdb=" OG1 THR D 706 " model vdw 2.170 2.440 nonbonded pdb=" O TYR B 702 " pdb=" OG1 THR B 706 " model vdw 2.170 2.440 nonbonded pdb=" OG1 THR D 220 " pdb=" OD1 ASN D 222 " model vdw 2.275 2.440 nonbonded pdb=" OG1 THR B 220 " pdb=" OD1 ASN B 222 " model vdw 2.276 2.440 nonbonded pdb=" O GLU D 225 " pdb=" OG SER D 229 " model vdw 2.283 2.440 ... (remaining 162194 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 148 through 533 or resid 547 through 791 or resid 1201)) selection = chain 'B' selection = (chain 'C' and (resid 148 through 533 or resid 547 through 791 or resid 1201)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.930 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 52.030 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.027 1.549 20824 Z= 1.811 Angle : 1.471 34.337 28272 Z= 0.794 Chirality : 0.213 5.651 3218 Planarity : 0.008 0.097 3512 Dihedral : 12.769 118.893 7646 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.64 % Allowed : 12.21 % Favored : 87.15 % Rotamer: Outliers : 0.72 % Allowed : 7.97 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.75 % 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: -5.63 (0.12), residues: 2482 helix: -3.95 (0.08), residues: 1346 sheet: -3.21 (0.49), residues: 74 loop : -3.31 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 733 HIS 0.005 0.001 HIS D 388 PHE 0.033 0.003 PHE D 185 TYR 0.025 0.002 TYR A 236 ARG 0.011 0.001 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 675 time to evaluate : 2.673 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: A 461 ASP cc_start: 0.8216 (t70) cc_final: 0.8011 (t70) REVERT: A 621 TYR cc_start: 0.8300 (t80) cc_final: 0.8026 (t80) REVERT: A 734 LYS cc_start: 0.8652 (tppp) cc_final: 0.8236 (tppt) REVERT: B 182 ASP cc_start: 0.6851 (m-30) cc_final: 0.6615 (m-30) REVERT: B 260 GLN cc_start: 0.8827 (mp-120) cc_final: 0.8603 (mp10) REVERT: B 457 GLU cc_start: 0.7447 (mp0) cc_final: 0.7091 (mp0) REVERT: B 549 PHE cc_start: 0.7035 (m-80) cc_final: 0.6740 (m-80) REVERT: B 612 LYS cc_start: 0.8740 (ttpm) cc_final: 0.8333 (ttpt) REVERT: B 625 MET cc_start: 0.8271 (ttp) cc_final: 0.7812 (mtp) REVERT: B 713 MET cc_start: 0.8605 (mmm) cc_final: 0.8275 (mmm) REVERT: C 621 TYR cc_start: 0.8260 (t80) cc_final: 0.7892 (t80) REVERT: C 635 LEU cc_start: 0.8464 (mt) cc_final: 0.8225 (mp) REVERT: C 685 MET cc_start: 0.6971 (tpt) cc_final: 0.6728 (ppp) REVERT: C 705 LEU cc_start: 0.8993 (mp) cc_final: 0.8680 (mp) REVERT: C 734 LYS cc_start: 0.8690 (tppp) cc_final: 0.8126 (tppt) REVERT: D 182 ASP cc_start: 0.6807 (m-30) cc_final: 0.6606 (m-30) REVERT: D 278 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6985 (tm-30) REVERT: D 346 TYR cc_start: 0.8118 (t80) cc_final: 0.7604 (t80) REVERT: D 457 GLU cc_start: 0.7594 (mp0) cc_final: 0.6940 (mp0) REVERT: D 461 ASP cc_start: 0.8261 (t70) cc_final: 0.7906 (t70) REVERT: D 517 THR cc_start: 0.8979 (m) cc_final: 0.8664 (p) REVERT: D 625 MET cc_start: 0.7947 (ttp) cc_final: 0.7469 (mtm) REVERT: D 730 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8773 (mmmt) outliers start: 16 outliers final: 2 residues processed: 685 average time/residue: 0.3338 time to fit residues: 340.7324 Evaluate side-chains 436 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 434 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain D residue 421 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 64 optimal weight: 30.0000 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 225 optimal weight: 0.6980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN A 228 ASN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN A 297 GLN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN A 474 ASN A 712 ASN B 204 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN B 326 HIS B 361 ASN B 401 HIS B 456 ASN B 492 GLN B 550 GLN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 ASN C 228 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN C 297 GLN C 456 ASN C 474 ASN C 712 ASN D 207 ASN D 222 ASN D 228 ASN D 326 HIS D 361 ASN D 401 HIS D 456 ASN ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 550 GLN D 787 HIS D 791 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.200 20824 Z= 0.409 Angle : 1.203 31.174 28272 Z= 0.536 Chirality : 0.087 2.278 3218 Planarity : 0.007 0.104 3512 Dihedral : 10.867 132.865 2888 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.60 % Allowed : 11.60 % Favored : 87.79 % Rotamer: Outliers : 4.35 % Allowed : 14.31 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.15), residues: 2482 helix: -2.12 (0.11), residues: 1356 sheet: -3.17 (0.50), residues: 74 loop : -2.91 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 737 HIS 0.005 0.001 HIS D 787 PHE 0.032 0.002 PHE A 341 TYR 0.027 0.002 TYR B 283 ARG 0.019 0.001 ARG D 757 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 460 time to evaluate : 2.147 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 156 ASP cc_start: 0.8139 (t70) cc_final: 0.7806 (t70) REVERT: A 234 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7833 (mm) REVERT: A 456 ASN cc_start: 0.8285 (t0) cc_final: 0.7936 (t0) REVERT: A 461 ASP cc_start: 0.8353 (t70) cc_final: 0.8081 (t70) REVERT: A 534 MET cc_start: 0.5908 (tpp) cc_final: 0.5077 (mtm) REVERT: A 559 LEU cc_start: 0.7502 (mp) cc_final: 0.7249 (tt) REVERT: A 577 VAL cc_start: 0.8825 (t) cc_final: 0.8495 (t) REVERT: A 591 TYR cc_start: 0.8383 (t80) cc_final: 0.7779 (t80) REVERT: A 713 MET cc_start: 0.8765 (mmm) cc_final: 0.8151 (mmt) REVERT: A 734 LYS cc_start: 0.8799 (tppp) cc_final: 0.8425 (tppt) REVERT: B 182 ASP cc_start: 0.6823 (m-30) cc_final: 0.6619 (m-30) REVERT: B 222 ASN cc_start: 0.7498 (p0) cc_final: 0.7079 (p0) REVERT: B 346 TYR cc_start: 0.7931 (t80) cc_final: 0.7321 (t80) REVERT: B 474 ASN cc_start: 0.8932 (m-40) cc_final: 0.8611 (m110) REVERT: B 549 PHE cc_start: 0.6918 (m-80) cc_final: 0.6670 (m-80) REVERT: B 605 MET cc_start: 0.8579 (tmm) cc_final: 0.7754 (tmm) REVERT: B 606 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7970 (pp) REVERT: B 610 LEU cc_start: 0.9052 (mm) cc_final: 0.8806 (mm) REVERT: B 685 MET cc_start: 0.4440 (ptt) cc_final: 0.4163 (ptm) REVERT: C 234 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7523 (mm) REVERT: C 491 TYR cc_start: 0.6741 (m-80) cc_final: 0.6410 (m-80) REVERT: C 685 MET cc_start: 0.7276 (tpt) cc_final: 0.6936 (ppp) REVERT: C 705 LEU cc_start: 0.8958 (mp) cc_final: 0.8743 (mp) REVERT: C 734 LYS cc_start: 0.8892 (tppp) cc_final: 0.8561 (tppt) REVERT: D 222 ASN cc_start: 0.7509 (OUTLIER) cc_final: 0.7196 (p0) REVERT: D 278 GLU cc_start: 0.7550 (tm-30) cc_final: 0.6711 (tm-30) REVERT: D 345 MET cc_start: 0.8647 (mtp) cc_final: 0.8388 (mtt) REVERT: D 346 TYR cc_start: 0.7929 (t80) cc_final: 0.7419 (t80) REVERT: D 400 ARG cc_start: 0.7382 (ttt-90) cc_final: 0.7110 (ttt-90) REVERT: D 461 ASP cc_start: 0.8388 (t70) cc_final: 0.7975 (t70) REVERT: D 517 THR cc_start: 0.8939 (m) cc_final: 0.8701 (p) REVERT: D 606 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7922 (pp) REVERT: D 730 LYS cc_start: 0.9014 (mmtt) cc_final: 0.8646 (mmmt) outliers start: 96 outliers final: 65 residues processed: 508 average time/residue: 0.2849 time to fit residues: 225.6687 Evaluate side-chains 474 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 404 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 461 ASP Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 574 TYR Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 704 ILE Chi-restraints excluded: chain D residue 709 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 30.0000 chunk 69 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 225 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 180 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN D 322 ASN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 787 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.262 20824 Z= 0.498 Angle : 1.271 29.532 28272 Z= 0.568 Chirality : 0.093 2.319 3218 Planarity : 0.008 0.191 3512 Dihedral : 10.754 133.040 2884 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.68 % Favored : 87.67 % Rotamer: Outliers : 4.89 % Allowed : 16.76 % Favored : 78.35 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.15), residues: 2482 helix: -1.81 (0.12), residues: 1352 sheet: -3.18 (0.50), residues: 74 loop : -2.90 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP B 776 HIS 0.003 0.001 HIS A 265 PHE 0.032 0.003 PHE D 524 TYR 0.027 0.002 TYR B 283 ARG 0.029 0.001 ARG C 616 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 414 time to evaluate : 2.361 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 156 ASP cc_start: 0.7989 (t70) cc_final: 0.7766 (t0) REVERT: A 234 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7831 (mm) REVERT: A 456 ASN cc_start: 0.8284 (t0) cc_final: 0.7937 (t0) REVERT: A 461 ASP cc_start: 0.8357 (t70) cc_final: 0.8072 (t70) REVERT: A 534 MET cc_start: 0.5918 (tpp) cc_final: 0.5176 (mtt) REVERT: A 559 LEU cc_start: 0.7485 (mp) cc_final: 0.7263 (tt) REVERT: A 577 VAL cc_start: 0.8829 (t) cc_final: 0.8514 (t) REVERT: A 591 TYR cc_start: 0.8382 (t80) cc_final: 0.7772 (t80) REVERT: A 685 MET cc_start: 0.7667 (tpp) cc_final: 0.7026 (ptp) REVERT: A 734 LYS cc_start: 0.8794 (tppp) cc_final: 0.8413 (tppt) REVERT: B 346 TYR cc_start: 0.7938 (t80) cc_final: 0.7265 (t80) REVERT: B 474 ASN cc_start: 0.8907 (m-40) cc_final: 0.8610 (m110) REVERT: B 549 PHE cc_start: 0.6873 (m-80) cc_final: 0.6657 (m-80) REVERT: B 575 LEU cc_start: 0.8075 (tt) cc_final: 0.7789 (tt) REVERT: B 605 MET cc_start: 0.8234 (tmm) cc_final: 0.8009 (tmm) REVERT: B 606 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8133 (pp) REVERT: B 685 MET cc_start: 0.4450 (ptt) cc_final: 0.4179 (ptm) REVERT: C 234 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7515 (mm) REVERT: C 456 ASN cc_start: 0.8399 (t0) cc_final: 0.7925 (t0) REVERT: C 685 MET cc_start: 0.7278 (tpt) cc_final: 0.6961 (ppp) REVERT: C 705 LEU cc_start: 0.8954 (mp) cc_final: 0.8744 (mp) REVERT: C 734 LYS cc_start: 0.8890 (tppp) cc_final: 0.8619 (tppt) REVERT: D 222 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7253 (p0) REVERT: D 278 GLU cc_start: 0.7565 (tm-30) cc_final: 0.6704 (tm-30) REVERT: D 345 MET cc_start: 0.8652 (mtp) cc_final: 0.8373 (mtt) REVERT: D 346 TYR cc_start: 0.7938 (t80) cc_final: 0.7263 (t80) REVERT: D 400 ARG cc_start: 0.7390 (ttt-90) cc_final: 0.7079 (ttt-90) REVERT: D 461 ASP cc_start: 0.8401 (t70) cc_final: 0.7978 (t70) REVERT: D 517 THR cc_start: 0.8933 (m) cc_final: 0.8706 (p) REVERT: D 621 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: D 625 MET cc_start: 0.7745 (mtp) cc_final: 0.7419 (mtm) REVERT: D 730 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8632 (mmmt) outliers start: 108 outliers final: 85 residues processed: 459 average time/residue: 0.2884 time to fit residues: 209.3914 Evaluate side-chains 493 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 403 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 461 ASP Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 669 PHE Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 574 TYR Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 621 TYR Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 704 ILE Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 chunk 64 optimal weight: 0.0470 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.262 20824 Z= 0.498 Angle : 1.271 29.532 28272 Z= 0.568 Chirality : 0.093 2.319 3218 Planarity : 0.008 0.191 3512 Dihedral : 10.754 133.040 2884 Min Nonbonded Distance : 1.517 Molprobity Statistics. All-atom Clashscore : 27.26 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.68 % Favored : 87.67 % Rotamer: Outliers : 4.08 % Allowed : 18.16 % Favored : 77.76 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.15), residues: 2482 helix: -1.81 (0.12), residues: 1352 sheet: -3.18 (0.50), residues: 74 loop : -2.90 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP B 776 HIS 0.003 0.001 HIS A 265 PHE 0.032 0.003 PHE D 524 TYR 0.027 0.002 TYR B 283 ARG 0.029 0.001 ARG C 616 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 404 time to evaluate : 2.203 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 234 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7831 (mm) REVERT: A 387 GLN cc_start: 0.8099 (tt0) cc_final: 0.7742 (tt0) REVERT: A 456 ASN cc_start: 0.8276 (t0) cc_final: 0.7937 (t0) REVERT: A 461 ASP cc_start: 0.8354 (t70) cc_final: 0.8071 (t70) REVERT: A 534 MET cc_start: 0.5918 (tpp) cc_final: 0.5177 (mtt) REVERT: A 559 LEU cc_start: 0.7482 (mp) cc_final: 0.7265 (tt) REVERT: A 577 VAL cc_start: 0.8832 (t) cc_final: 0.8515 (t) REVERT: A 591 TYR cc_start: 0.8378 (t80) cc_final: 0.7773 (t80) REVERT: A 685 MET cc_start: 0.7667 (tpp) cc_final: 0.7026 (ptp) REVERT: A 734 LYS cc_start: 0.8799 (tppp) cc_final: 0.8409 (tppt) REVERT: B 346 TYR cc_start: 0.7942 (t80) cc_final: 0.7264 (t80) REVERT: B 474 ASN cc_start: 0.8907 (m-40) cc_final: 0.8610 (m110) REVERT: B 549 PHE cc_start: 0.6880 (m-80) cc_final: 0.6657 (m-80) REVERT: B 575 LEU cc_start: 0.8075 (tt) cc_final: 0.7788 (tt) REVERT: B 685 MET cc_start: 0.4454 (ptt) cc_final: 0.4175 (ptm) REVERT: C 234 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7515 (mm) REVERT: C 456 ASN cc_start: 0.8403 (t0) cc_final: 0.7926 (t0) REVERT: C 685 MET cc_start: 0.7278 (tpt) cc_final: 0.6962 (ppp) REVERT: C 705 LEU cc_start: 0.8953 (mp) cc_final: 0.8744 (mp) REVERT: C 734 LYS cc_start: 0.8892 (tppp) cc_final: 0.8619 (tppt) REVERT: D 222 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.7253 (p0) REVERT: D 278 GLU cc_start: 0.7565 (tm-30) cc_final: 0.6704 (tm-30) REVERT: D 345 MET cc_start: 0.8643 (mtp) cc_final: 0.8373 (mtt) REVERT: D 346 TYR cc_start: 0.7937 (t80) cc_final: 0.7263 (t80) REVERT: D 400 ARG cc_start: 0.7388 (ttt-90) cc_final: 0.7080 (ttt-90) REVERT: D 461 ASP cc_start: 0.8397 (t70) cc_final: 0.7978 (t70) REVERT: D 517 THR cc_start: 0.8946 (m) cc_final: 0.8707 (p) REVERT: D 621 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: D 625 MET cc_start: 0.7749 (mtp) cc_final: 0.7420 (mtm) REVERT: D 730 LYS cc_start: 0.9005 (mmtt) cc_final: 0.8632 (mmmt) outliers start: 90 outliers final: 85 residues processed: 437 average time/residue: 0.2799 time to fit residues: 194.2583 Evaluate side-chains 490 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 401 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 461 ASP Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 669 PHE Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 574 TYR Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 621 TYR Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 704 ILE Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 178 optimal weight: 0.0980 chunk 98 optimal weight: 0.0970 chunk 204 optimal weight: 0.1980 chunk 165 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN ** D 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.262 20824 Z= 0.497 Angle : 1.270 29.519 28272 Z= 0.568 Chirality : 0.093 2.319 3218 Planarity : 0.008 0.191 3512 Dihedral : 10.757 133.040 2884 Min Nonbonded Distance : 1.518 Molprobity Statistics. All-atom Clashscore : 27.85 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.68 % Favored : 87.67 % Rotamer: Outliers : 4.08 % Allowed : 18.34 % Favored : 77.58 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.15), residues: 2482 helix: -1.81 (0.12), residues: 1352 sheet: -3.18 (0.50), residues: 74 loop : -2.90 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP B 776 HIS 0.003 0.001 HIS A 265 PHE 0.032 0.003 PHE D 524 TYR 0.027 0.002 TYR B 283 ARG 0.029 0.001 ARG C 616 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 401 time to evaluate : 2.419 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 234 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7831 (mm) REVERT: A 387 GLN cc_start: 0.8099 (tt0) cc_final: 0.7742 (tt0) REVERT: A 456 ASN cc_start: 0.8276 (t0) cc_final: 0.7937 (t0) REVERT: A 461 ASP cc_start: 0.8354 (t70) cc_final: 0.8071 (t70) REVERT: A 534 MET cc_start: 0.5919 (tpp) cc_final: 0.5177 (mtt) REVERT: A 559 LEU cc_start: 0.7482 (mp) cc_final: 0.7265 (tt) REVERT: A 577 VAL cc_start: 0.8832 (t) cc_final: 0.8515 (t) REVERT: A 591 TYR cc_start: 0.8378 (t80) cc_final: 0.7773 (t80) REVERT: A 685 MET cc_start: 0.7667 (tpp) cc_final: 0.7026 (ptp) REVERT: A 734 LYS cc_start: 0.8799 (tppp) cc_final: 0.8408 (tppt) REVERT: B 346 TYR cc_start: 0.7942 (t80) cc_final: 0.7264 (t80) REVERT: B 474 ASN cc_start: 0.8907 (m-40) cc_final: 0.8610 (m110) REVERT: B 549 PHE cc_start: 0.6880 (m-80) cc_final: 0.6657 (m-80) REVERT: B 575 LEU cc_start: 0.8075 (tt) cc_final: 0.7788 (tt) REVERT: B 685 MET cc_start: 0.4454 (ptt) cc_final: 0.4175 (ptm) REVERT: C 234 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7515 (mm) REVERT: C 456 ASN cc_start: 0.8402 (t0) cc_final: 0.7926 (t0) REVERT: C 685 MET cc_start: 0.7279 (tpt) cc_final: 0.6962 (ppp) REVERT: C 705 LEU cc_start: 0.8953 (mp) cc_final: 0.8744 (mp) REVERT: C 734 LYS cc_start: 0.8891 (tppp) cc_final: 0.8618 (tppt) REVERT: D 222 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.7253 (p0) REVERT: D 278 GLU cc_start: 0.7564 (tm-30) cc_final: 0.6704 (tm-30) REVERT: D 345 MET cc_start: 0.8643 (mtp) cc_final: 0.8373 (mtt) REVERT: D 346 TYR cc_start: 0.7937 (t80) cc_final: 0.7262 (t80) REVERT: D 400 ARG cc_start: 0.7388 (ttt-90) cc_final: 0.7080 (ttt-90) REVERT: D 461 ASP cc_start: 0.8397 (t70) cc_final: 0.7978 (t70) REVERT: D 517 THR cc_start: 0.8946 (m) cc_final: 0.8707 (p) REVERT: D 621 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: D 625 MET cc_start: 0.7750 (mtp) cc_final: 0.7420 (mtm) REVERT: D 730 LYS cc_start: 0.9005 (mmtt) cc_final: 0.8632 (mmmt) outliers start: 90 outliers final: 85 residues processed: 433 average time/residue: 0.2777 time to fit residues: 191.7307 Evaluate side-chains 490 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 401 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 461 ASP Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 669 PHE Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 574 TYR Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 621 TYR Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 704 ILE Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 140 optimal weight: 0.1980 chunk 59 optimal weight: 0.9990 chunk 239 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 79 optimal weight: 0.0970 chunk 125 optimal weight: 20.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN ** D 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.258 20824 Z= 0.494 Angle : 1.275 29.333 28272 Z= 0.569 Chirality : 0.093 2.323 3218 Planarity : 0.008 0.192 3512 Dihedral : 10.753 133.041 2884 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 28.00 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.68 % Favored : 87.67 % Rotamer: Outliers : 4.08 % Allowed : 18.25 % Favored : 77.67 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.15), residues: 2482 helix: -1.81 (0.12), residues: 1352 sheet: -3.18 (0.50), residues: 74 loop : -2.90 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP B 776 HIS 0.003 0.001 HIS A 265 PHE 0.032 0.003 PHE D 524 TYR 0.027 0.002 TYR B 283 ARG 0.029 0.001 ARG C 616 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 401 time to evaluate : 2.251 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 234 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7831 (mm) REVERT: A 387 GLN cc_start: 0.8099 (tt0) cc_final: 0.7744 (tt0) REVERT: A 456 ASN cc_start: 0.8276 (t0) cc_final: 0.7937 (t0) REVERT: A 461 ASP cc_start: 0.8353 (t70) cc_final: 0.8070 (t70) REVERT: A 534 MET cc_start: 0.5919 (tpp) cc_final: 0.5177 (mtt) REVERT: A 559 LEU cc_start: 0.7482 (mp) cc_final: 0.7265 (tt) REVERT: A 577 VAL cc_start: 0.8832 (t) cc_final: 0.8515 (t) REVERT: A 591 TYR cc_start: 0.8378 (t80) cc_final: 0.7773 (t80) REVERT: A 685 MET cc_start: 0.7667 (tpp) cc_final: 0.7026 (ptp) REVERT: A 734 LYS cc_start: 0.8799 (tppp) cc_final: 0.8408 (tppt) REVERT: B 346 TYR cc_start: 0.7942 (t80) cc_final: 0.7262 (t80) REVERT: B 474 ASN cc_start: 0.8907 (m-40) cc_final: 0.8610 (m110) REVERT: B 549 PHE cc_start: 0.6880 (m-80) cc_final: 0.6655 (m-80) REVERT: B 575 LEU cc_start: 0.8075 (tt) cc_final: 0.7788 (tt) REVERT: B 685 MET cc_start: 0.4453 (ptt) cc_final: 0.4175 (ptm) REVERT: C 234 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7515 (mm) REVERT: C 456 ASN cc_start: 0.8402 (t0) cc_final: 0.7926 (t0) REVERT: C 685 MET cc_start: 0.7279 (tpt) cc_final: 0.6961 (ppp) REVERT: C 705 LEU cc_start: 0.8953 (mp) cc_final: 0.8744 (mp) REVERT: C 734 LYS cc_start: 0.8896 (tppp) cc_final: 0.8621 (tppt) REVERT: D 222 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7254 (p0) REVERT: D 278 GLU cc_start: 0.7565 (tm-30) cc_final: 0.6704 (tm-30) REVERT: D 345 MET cc_start: 0.8643 (mtp) cc_final: 0.8372 (mtt) REVERT: D 346 TYR cc_start: 0.7937 (t80) cc_final: 0.7261 (t80) REVERT: D 400 ARG cc_start: 0.7388 (ttt-90) cc_final: 0.7079 (ttt-90) REVERT: D 461 ASP cc_start: 0.8398 (t70) cc_final: 0.7978 (t70) REVERT: D 517 THR cc_start: 0.8946 (m) cc_final: 0.8706 (p) REVERT: D 621 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: D 625 MET cc_start: 0.7750 (mtp) cc_final: 0.7420 (mtm) REVERT: D 730 LYS cc_start: 0.9005 (mmtt) cc_final: 0.8632 (mmmt) outliers start: 90 outliers final: 85 residues processed: 434 average time/residue: 0.3096 time to fit residues: 214.1133 Evaluate side-chains 491 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 402 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 461 ASP Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 669 PHE Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 563 SER Chi-restraints excluded: chain D residue 574 TYR Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 621 TYR Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 704 ILE Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 709 LEU Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 201 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 239 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN B 207 ASN B 322 ASN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.169 20824 Z= 0.390 Angle : 1.219 28.164 28272 Z= 0.544 Chirality : 0.095 2.398 3218 Planarity : 0.007 0.192 3512 Dihedral : 10.664 133.016 2884 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.72 % Favored : 87.63 % Rotamer: Outliers : 4.80 % Allowed : 17.53 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.15), residues: 2482 helix: -1.68 (0.12), residues: 1366 sheet: -2.94 (0.52), residues: 70 loop : -2.93 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 776 HIS 0.004 0.001 HIS B 447 PHE 0.026 0.002 PHE A 341 TYR 0.026 0.002 TYR B 283 ARG 0.052 0.001 ARG B 757 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 411 time to evaluate : 2.475 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 223 MET cc_start: 0.8079 (ttm) cc_final: 0.7589 (ttm) REVERT: A 234 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7829 (mm) REVERT: A 456 ASN cc_start: 0.8270 (t0) cc_final: 0.7932 (t0) REVERT: A 461 ASP cc_start: 0.8336 (t70) cc_final: 0.8064 (t70) REVERT: A 480 CYS cc_start: 0.8300 (m) cc_final: 0.7940 (t) REVERT: A 534 MET cc_start: 0.5958 (tpp) cc_final: 0.5198 (mtt) REVERT: A 559 LEU cc_start: 0.7431 (mp) cc_final: 0.7205 (tt) REVERT: A 577 VAL cc_start: 0.8833 (t) cc_final: 0.8520 (t) REVERT: A 591 TYR cc_start: 0.8382 (t80) cc_final: 0.7710 (t80) REVERT: A 685 MET cc_start: 0.7691 (tpp) cc_final: 0.7044 (ptp) REVERT: A 734 LYS cc_start: 0.8795 (tppp) cc_final: 0.8404 (tppt) REVERT: B 346 TYR cc_start: 0.7951 (t80) cc_final: 0.7253 (t80) REVERT: B 457 GLU cc_start: 0.7559 (mp0) cc_final: 0.6993 (mp0) REVERT: B 474 ASN cc_start: 0.8896 (m-40) cc_final: 0.8605 (m110) REVERT: B 549 PHE cc_start: 0.6824 (m-80) cc_final: 0.6610 (m-80) REVERT: B 575 LEU cc_start: 0.8090 (tt) cc_final: 0.7778 (tt) REVERT: B 685 MET cc_start: 0.4434 (ptt) cc_final: 0.4182 (ptm) REVERT: C 219 ARG cc_start: 0.8313 (mmm160) cc_final: 0.8014 (mmm160) REVERT: C 234 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7516 (mm) REVERT: C 456 ASN cc_start: 0.8392 (t0) cc_final: 0.7912 (t0) REVERT: C 685 MET cc_start: 0.7282 (tpt) cc_final: 0.6982 (ppp) REVERT: C 705 LEU cc_start: 0.8966 (mp) cc_final: 0.8753 (mp) REVERT: C 734 LYS cc_start: 0.8884 (tppp) cc_final: 0.8594 (tppt) REVERT: D 278 GLU cc_start: 0.7558 (tm-30) cc_final: 0.6958 (tm-30) REVERT: D 287 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8448 (mp) REVERT: D 345 MET cc_start: 0.8626 (mtp) cc_final: 0.8341 (mtt) REVERT: D 346 TYR cc_start: 0.7947 (t80) cc_final: 0.7249 (t80) REVERT: D 461 ASP cc_start: 0.8390 (t70) cc_final: 0.7970 (t70) REVERT: D 517 THR cc_start: 0.8934 (m) cc_final: 0.8690 (p) REVERT: D 524 PHE cc_start: 0.8513 (m-80) cc_final: 0.7916 (t80) REVERT: D 557 SER cc_start: 0.8776 (p) cc_final: 0.8466 (t) REVERT: D 621 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.7013 (m-80) REVERT: D 625 MET cc_start: 0.7803 (mtp) cc_final: 0.7348 (mtm) REVERT: D 730 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8619 (mmmt) outliers start: 106 outliers final: 82 residues processed: 454 average time/residue: 0.2831 time to fit residues: 203.4729 Evaluate side-chains 490 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 404 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 461 ASP Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 669 PHE Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 621 TYR Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 704 ILE Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 22 optimal weight: 0.5980 chunk 187 optimal weight: 10.0000 chunk 217 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.169 20824 Z= 0.390 Angle : 1.219 28.164 28272 Z= 0.544 Chirality : 0.095 2.398 3218 Planarity : 0.007 0.192 3512 Dihedral : 10.664 133.016 2884 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 24.56 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.72 % Favored : 87.63 % Rotamer: Outliers : 3.89 % Allowed : 18.61 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.15), residues: 2482 helix: -1.68 (0.12), residues: 1366 sheet: -2.94 (0.52), residues: 70 loop : -2.93 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 776 HIS 0.004 0.001 HIS B 447 PHE 0.026 0.002 PHE A 341 TYR 0.026 0.002 TYR B 283 ARG 0.052 0.001 ARG B 757 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 404 time to evaluate : 2.403 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 223 MET cc_start: 0.8079 (ttm) cc_final: 0.7588 (ttm) REVERT: A 234 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7829 (mm) REVERT: A 456 ASN cc_start: 0.8272 (t0) cc_final: 0.7932 (t0) REVERT: A 461 ASP cc_start: 0.8338 (t70) cc_final: 0.8064 (t70) REVERT: A 480 CYS cc_start: 0.8298 (m) cc_final: 0.7940 (t) REVERT: A 534 MET cc_start: 0.5961 (tpp) cc_final: 0.5199 (mtt) REVERT: A 559 LEU cc_start: 0.7432 (mp) cc_final: 0.7205 (tt) REVERT: A 577 VAL cc_start: 0.8832 (t) cc_final: 0.8520 (t) REVERT: A 591 TYR cc_start: 0.8383 (t80) cc_final: 0.7711 (t80) REVERT: A 685 MET cc_start: 0.7691 (tpp) cc_final: 0.7044 (ptp) REVERT: A 734 LYS cc_start: 0.8795 (tppp) cc_final: 0.8404 (tppt) REVERT: B 346 TYR cc_start: 0.7959 (t80) cc_final: 0.7254 (t80) REVERT: B 457 GLU cc_start: 0.7560 (mp0) cc_final: 0.6993 (mp0) REVERT: B 474 ASN cc_start: 0.8894 (m-40) cc_final: 0.8605 (m110) REVERT: B 549 PHE cc_start: 0.6825 (m-80) cc_final: 0.6608 (m-80) REVERT: B 575 LEU cc_start: 0.8090 (tt) cc_final: 0.7778 (tt) REVERT: B 685 MET cc_start: 0.4432 (ptt) cc_final: 0.4181 (ptm) REVERT: C 219 ARG cc_start: 0.8299 (mmm160) cc_final: 0.8015 (mmm160) REVERT: C 234 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7516 (mm) REVERT: C 456 ASN cc_start: 0.8392 (t0) cc_final: 0.7913 (t0) REVERT: C 685 MET cc_start: 0.7283 (tpt) cc_final: 0.6982 (ppp) REVERT: C 705 LEU cc_start: 0.8966 (mp) cc_final: 0.8752 (mp) REVERT: C 734 LYS cc_start: 0.8875 (tppp) cc_final: 0.8594 (tppt) REVERT: D 278 GLU cc_start: 0.7565 (tm-30) cc_final: 0.6958 (tm-30) REVERT: D 287 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8449 (mp) REVERT: D 345 MET cc_start: 0.8626 (mtp) cc_final: 0.8341 (mtt) REVERT: D 346 TYR cc_start: 0.7946 (t80) cc_final: 0.7250 (t80) REVERT: D 461 ASP cc_start: 0.8393 (t70) cc_final: 0.7970 (t70) REVERT: D 517 THR cc_start: 0.8935 (m) cc_final: 0.8690 (p) REVERT: D 524 PHE cc_start: 0.8513 (m-80) cc_final: 0.7916 (t80) REVERT: D 557 SER cc_start: 0.8776 (p) cc_final: 0.8467 (t) REVERT: D 621 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.7014 (m-80) REVERT: D 625 MET cc_start: 0.7801 (mtp) cc_final: 0.7348 (mtm) REVERT: D 730 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8620 (mmmt) outliers start: 86 outliers final: 82 residues processed: 436 average time/residue: 0.2838 time to fit residues: 197.5393 Evaluate side-chains 490 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 404 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 461 ASP Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 669 PHE Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 621 TYR Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 704 ILE Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.9990 chunk 208 optimal weight: 6.9990 chunk 222 optimal weight: 0.0270 chunk 134 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 201 optimal weight: 0.5980 chunk 210 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.169 20824 Z= 0.390 Angle : 1.219 28.164 28272 Z= 0.544 Chirality : 0.095 2.398 3218 Planarity : 0.007 0.192 3512 Dihedral : 10.666 133.016 2884 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 24.90 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.72 % Favored : 87.63 % Rotamer: Outliers : 3.94 % Allowed : 18.70 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.15), residues: 2482 helix: -1.68 (0.12), residues: 1366 sheet: -2.94 (0.52), residues: 70 loop : -2.93 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 776 HIS 0.004 0.001 HIS B 447 PHE 0.026 0.002 PHE A 341 TYR 0.026 0.002 TYR B 283 ARG 0.052 0.001 ARG B 757 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 404 time to evaluate : 2.121 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 223 MET cc_start: 0.8079 (ttm) cc_final: 0.7588 (ttm) REVERT: A 234 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7829 (mm) REVERT: A 456 ASN cc_start: 0.8272 (t0) cc_final: 0.7932 (t0) REVERT: A 461 ASP cc_start: 0.8338 (t70) cc_final: 0.8064 (t70) REVERT: A 480 CYS cc_start: 0.8298 (m) cc_final: 0.7940 (t) REVERT: A 534 MET cc_start: 0.5962 (tpp) cc_final: 0.5199 (mtt) REVERT: A 559 LEU cc_start: 0.7432 (mp) cc_final: 0.7205 (tt) REVERT: A 577 VAL cc_start: 0.8833 (t) cc_final: 0.8521 (t) REVERT: A 591 TYR cc_start: 0.8383 (t80) cc_final: 0.7711 (t80) REVERT: A 685 MET cc_start: 0.7691 (tpp) cc_final: 0.7044 (ptp) REVERT: A 734 LYS cc_start: 0.8795 (tppp) cc_final: 0.8404 (tppt) REVERT: B 346 TYR cc_start: 0.7960 (t80) cc_final: 0.7253 (t80) REVERT: B 449 MET cc_start: 0.8510 (mtp) cc_final: 0.8280 (mtm) REVERT: B 457 GLU cc_start: 0.7560 (mp0) cc_final: 0.6993 (mp0) REVERT: B 474 ASN cc_start: 0.8894 (m-40) cc_final: 0.8606 (m110) REVERT: B 549 PHE cc_start: 0.6823 (m-80) cc_final: 0.6608 (m-80) REVERT: B 575 LEU cc_start: 0.8090 (tt) cc_final: 0.7778 (tt) REVERT: B 685 MET cc_start: 0.4432 (ptt) cc_final: 0.4181 (ptm) REVERT: C 219 ARG cc_start: 0.8300 (mmm160) cc_final: 0.8014 (mmm160) REVERT: C 234 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7516 (mm) REVERT: C 456 ASN cc_start: 0.8392 (t0) cc_final: 0.7912 (t0) REVERT: C 685 MET cc_start: 0.7282 (tpt) cc_final: 0.6982 (ppp) REVERT: C 705 LEU cc_start: 0.8966 (mp) cc_final: 0.8752 (mp) REVERT: C 734 LYS cc_start: 0.8875 (tppp) cc_final: 0.8594 (tppt) REVERT: D 278 GLU cc_start: 0.7565 (tm-30) cc_final: 0.6958 (tm-30) REVERT: D 287 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8448 (mp) REVERT: D 345 MET cc_start: 0.8625 (mtp) cc_final: 0.8341 (mtt) REVERT: D 346 TYR cc_start: 0.7947 (t80) cc_final: 0.7250 (t80) REVERT: D 461 ASP cc_start: 0.8393 (t70) cc_final: 0.7970 (t70) REVERT: D 517 THR cc_start: 0.8935 (m) cc_final: 0.8690 (p) REVERT: D 524 PHE cc_start: 0.8513 (m-80) cc_final: 0.7916 (t80) REVERT: D 557 SER cc_start: 0.8777 (p) cc_final: 0.8467 (t) REVERT: D 621 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.7014 (m-80) REVERT: D 625 MET cc_start: 0.7801 (mtp) cc_final: 0.7348 (mtm) REVERT: D 730 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8619 (mmmt) outliers start: 87 outliers final: 82 residues processed: 436 average time/residue: 0.2967 time to fit residues: 205.9192 Evaluate side-chains 490 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 404 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 461 ASP Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 669 PHE Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 621 TYR Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 704 ILE Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.9980 chunk 143 optimal weight: 0.0980 chunk 111 optimal weight: 5.9990 chunk 163 optimal weight: 30.0000 chunk 247 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.168 20824 Z= 0.390 Angle : 1.219 28.163 28272 Z= 0.544 Chirality : 0.095 2.397 3218 Planarity : 0.007 0.192 3512 Dihedral : 10.659 133.017 2884 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 24.90 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.72 % Favored : 87.63 % Rotamer: Outliers : 3.89 % Allowed : 18.70 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.15), residues: 2482 helix: -1.68 (0.12), residues: 1366 sheet: -2.94 (0.52), residues: 70 loop : -2.93 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 776 HIS 0.004 0.001 HIS B 447 PHE 0.026 0.002 PHE A 341 TYR 0.026 0.002 TYR B 283 ARG 0.052 0.001 ARG B 757 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4964 Ramachandran restraints generated. 2482 Oldfield, 0 Emsley, 2482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 404 time to evaluate : 2.277 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 223 MET cc_start: 0.8079 (ttm) cc_final: 0.7588 (ttm) REVERT: A 234 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7829 (mm) REVERT: A 456 ASN cc_start: 0.8272 (t0) cc_final: 0.7932 (t0) REVERT: A 461 ASP cc_start: 0.8338 (t70) cc_final: 0.8064 (t70) REVERT: A 480 CYS cc_start: 0.8298 (m) cc_final: 0.7940 (t) REVERT: A 534 MET cc_start: 0.5962 (tpp) cc_final: 0.5199 (mtt) REVERT: A 559 LEU cc_start: 0.7432 (mp) cc_final: 0.7205 (tt) REVERT: A 577 VAL cc_start: 0.8833 (t) cc_final: 0.8520 (t) REVERT: A 591 TYR cc_start: 0.8383 (t80) cc_final: 0.7711 (t80) REVERT: A 685 MET cc_start: 0.7691 (tpp) cc_final: 0.7044 (ptp) REVERT: A 734 LYS cc_start: 0.8795 (tppp) cc_final: 0.8404 (tppt) REVERT: B 346 TYR cc_start: 0.7960 (t80) cc_final: 0.7253 (t80) REVERT: B 449 MET cc_start: 0.8510 (mtp) cc_final: 0.8280 (mtm) REVERT: B 457 GLU cc_start: 0.7560 (mp0) cc_final: 0.6993 (mp0) REVERT: B 474 ASN cc_start: 0.8894 (m-40) cc_final: 0.8606 (m110) REVERT: B 549 PHE cc_start: 0.6822 (m-80) cc_final: 0.6608 (m-80) REVERT: B 575 LEU cc_start: 0.8090 (tt) cc_final: 0.7778 (tt) REVERT: B 685 MET cc_start: 0.4432 (ptt) cc_final: 0.4181 (ptm) REVERT: C 219 ARG cc_start: 0.8300 (mmm160) cc_final: 0.8015 (mmm160) REVERT: C 234 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7516 (mm) REVERT: C 456 ASN cc_start: 0.8392 (t0) cc_final: 0.7913 (t0) REVERT: C 685 MET cc_start: 0.7282 (tpt) cc_final: 0.6982 (ppp) REVERT: C 705 LEU cc_start: 0.8966 (mp) cc_final: 0.8752 (mp) REVERT: C 734 LYS cc_start: 0.8875 (tppp) cc_final: 0.8594 (tppt) REVERT: D 278 GLU cc_start: 0.7565 (tm-30) cc_final: 0.6958 (tm-30) REVERT: D 287 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8449 (mp) REVERT: D 345 MET cc_start: 0.8625 (mtp) cc_final: 0.8341 (mtt) REVERT: D 346 TYR cc_start: 0.7947 (t80) cc_final: 0.7250 (t80) REVERT: D 461 ASP cc_start: 0.8393 (t70) cc_final: 0.7970 (t70) REVERT: D 517 THR cc_start: 0.8935 (m) cc_final: 0.8690 (p) REVERT: D 524 PHE cc_start: 0.8513 (m-80) cc_final: 0.7916 (t80) REVERT: D 557 SER cc_start: 0.8776 (p) cc_final: 0.8466 (t) REVERT: D 621 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.7014 (m-80) REVERT: D 625 MET cc_start: 0.7801 (mtp) cc_final: 0.7348 (mtm) REVERT: D 730 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8619 (mmmt) outliers start: 86 outliers final: 82 residues processed: 436 average time/residue: 0.2856 time to fit residues: 197.2022 Evaluate side-chains 490 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 404 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 357 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 639 CYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 252 HIS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 357 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 461 ASP Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 669 PHE Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 252 HIS Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 432 SER Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 621 TYR Chi-restraints excluded: chain D residue 630 SER Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 704 ILE Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 714 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 202 optimal weight: 0.9980 chunk 24 optimal weight: 0.0020 chunk 36 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN D 222 ASN D 322 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.183774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.132212 restraints weight = 43658.378| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.85 r_work: 0.3484 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.261 20824 Z= 0.422 Angle : 1.230 27.775 28272 Z= 0.547 Chirality : 0.097 2.426 3218 Planarity : 0.006 0.106 3512 Dihedral : 10.598 133.184 2884 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.68 % Allowed : 11.85 % Favored : 87.47 % Rotamer: Outliers : 4.12 % Allowed : 18.48 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.15), residues: 2482 helix: -1.57 (0.12), residues: 1368 sheet: -3.15 (0.50), residues: 74 loop : -2.89 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 776 HIS 0.005 0.001 HIS A 265 PHE 0.027 0.002 PHE A 341 TYR 0.034 0.002 TYR C 439 ARG 0.039 0.001 ARG B 757 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4915.36 seconds wall clock time: 89 minutes 17.76 seconds (5357.76 seconds total)