Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 10:29:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/08_2023/8t1d_40960_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/08_2023/8t1d_40960.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/08_2023/8t1d_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_40960/08_2023/8t1d_40960_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/08_2023/8t1d_40960_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/08_2023/8t1d_40960.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/08_2023/8t1d_40960.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/08_2023/8t1d_40960_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1d_40960/08_2023/8t1d_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 10.11, per 1000 atoms: 0.50 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: 8.20 Conformation dependent library (CDL) restraints added in 2.8 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: 3.49 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: 5.39 Time building geometry restraints manager: 8.81 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 - 21.75: 11736 21.75 - 43.51: 528 43.51 - 65.26: 64 65.26 - 87.01: 8 87.01 - 108.76: 2 Dihedral angle restraints: 12338 sinusoidal: 5002 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 12335 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: 1.750 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: 8.640 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 50.780 Find NCS groups from input model: 1.490 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.150 ------------------------------------------------------------------------------- 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 : 12.154 108.765 7598 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 % 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 *********************** 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 : 2.277 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 685 average time/residue: 0.3481 time to fit residues: 356.3059 Evaluate side-chains 426 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 424 time to evaluate : 2.218 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1822 time to fit residues: 3.7680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.146 20824 Z= 0.389 Angle : 1.168 30.633 28272 Z= 0.525 Chirality : 0.092 2.368 3218 Planarity : 0.007 0.091 3512 Dihedral : 9.445 134.162 2836 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.80 % Favored : 87.55 % Rotamer Outliers : 4.39 % 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: -3.75 (0.15), residues: 2482 helix: -2.10 (0.11), residues: 1354 sheet: -3.24 (0.50), residues: 74 loop : -2.87 (0.19), residues: 1054 *********************** 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 546 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 449 time to evaluate : 2.216 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 outliers start: 97 outliers final: 65 residues processed: 500 average time/residue: 0.2958 time to fit residues: 231.0065 Evaluate side-chains 462 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 397 time to evaluate : 2.431 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.1904 time to fit residues: 26.0406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 180 optimal weight: 20.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 322 ASN B 736 GLN C 260 GLN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D 492 GLN D 787 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.123 20824 Z= 0.333 Angle : 1.095 25.531 28272 Z= 0.490 Chirality : 0.096 2.467 3218 Planarity : 0.006 0.099 3512 Dihedral : 9.122 132.893 2836 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.21 % Favored : 87.23 % Rotamer Outliers : 2.63 % 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: -3.06 (0.16), residues: 2482 helix: -1.35 (0.13), residues: 1354 sheet: -3.14 (0.50), residues: 74 loop : -2.82 (0.19), residues: 1054 *********************** 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 488 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 430 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 27 residues processed: 458 average time/residue: 0.2960 time to fit residues: 215.0854 Evaluate side-chains 428 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 401 time to evaluate : 2.439 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 27 outliers final: 1 residues processed: 27 average time/residue: 0.1889 time to fit residues: 12.4913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 107 optimal weight: 0.1980 chunk 151 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 239 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN B 736 GLN B 791 ASN C 201 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.106 20824 Z= 0.293 Angle : 1.074 26.401 28272 Z= 0.474 Chirality : 0.095 2.422 3218 Planarity : 0.006 0.129 3512 Dihedral : 8.972 136.643 2836 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.76 % Favored : 87.67 % Rotamer Outliers : 3.17 % 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: -2.81 (0.16), residues: 2482 helix: -1.10 (0.13), residues: 1372 sheet: -3.08 (0.51), residues: 74 loop : -2.78 (0.19), residues: 1036 *********************** 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 479 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 409 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 39 residues processed: 435 average time/residue: 0.2839 time to fit residues: 197.9025 Evaluate side-chains 429 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 390 time to evaluate : 2.280 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 39 outliers final: 1 residues processed: 39 average time/residue: 0.1933 time to fit residues: 17.3135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 204 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 215 optimal weight: 0.0970 chunk 60 optimal weight: 5.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN D 492 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.108 20824 Z= 0.282 Angle : 1.050 25.779 28272 Z= 0.464 Chirality : 0.093 2.376 3218 Planarity : 0.005 0.080 3512 Dihedral : 8.809 138.004 2836 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.93 % Favored : 87.51 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.16), residues: 2482 helix: -0.97 (0.13), residues: 1376 sheet: -3.00 (0.51), residues: 74 loop : -2.77 (0.20), residues: 1032 *********************** 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 447 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 410 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 25 residues processed: 422 average time/residue: 0.2826 time to fit residues: 191.3525 Evaluate side-chains 416 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 391 time to evaluate : 2.052 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1915 time to fit residues: 11.9241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 0.2980 chunk 47 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 239 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 79 optimal weight: 0.4980 chunk 125 optimal weight: 20.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 ASN C 387 GLN D 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.237 20824 Z= 0.379 Angle : 1.069 25.692 28272 Z= 0.475 Chirality : 0.092 2.326 3218 Planarity : 0.005 0.079 3512 Dihedral : 8.780 138.024 2836 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.60 % Allowed : 11.89 % Favored : 87.51 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.16), residues: 2482 helix: -0.95 (0.13), residues: 1376 sheet: -3.00 (0.51), residues: 74 loop : -2.76 (0.20), residues: 1032 *********************** 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 443 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 404 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 26 residues processed: 417 average time/residue: 0.2869 time to fit residues: 192.3229 Evaluate side-chains 420 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 394 time to evaluate : 2.255 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1933 time to fit residues: 12.5672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0050 chunk 136 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 239 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 ASN C 387 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 20824 Z= 0.257 Angle : 1.046 25.892 28272 Z= 0.461 Chirality : 0.092 2.400 3218 Planarity : 0.005 0.076 3512 Dihedral : 8.701 138.966 2836 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.52 % Favored : 87.91 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.16), residues: 2482 helix: -0.81 (0.13), residues: 1378 sheet: -2.92 (0.52), residues: 74 loop : -2.67 (0.20), residues: 1030 *********************** 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 437 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 411 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 418 average time/residue: 0.2971 time to fit residues: 197.7787 Evaluate side-chains 411 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 396 time to evaluate : 2.252 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1871 time to fit residues: 8.3451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 217 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.100 20824 Z= 0.290 Angle : 1.043 25.721 28272 Z= 0.462 Chirality : 0.093 2.390 3218 Planarity : 0.005 0.076 3512 Dihedral : 8.557 139.573 2836 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.97 % Favored : 87.47 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.17), residues: 2482 helix: -0.73 (0.13), residues: 1388 sheet: -2.89 (0.52), residues: 74 loop : -2.61 (0.20), residues: 1020 *********************** 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 443 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 407 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 25 residues processed: 414 average time/residue: 0.3060 time to fit residues: 202.2414 Evaluate side-chains 417 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 392 time to evaluate : 2.210 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1778 time to fit residues: 11.4698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 chunk 222 optimal weight: 0.0470 chunk 134 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 174 optimal weight: 0.0970 chunk 68 optimal weight: 6.9990 chunk 201 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN C 260 GLN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN D 222 ASN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 20824 Z= 0.246 Angle : 1.033 25.966 28272 Z= 0.453 Chirality : 0.092 2.331 3218 Planarity : 0.005 0.073 3512 Dihedral : 8.506 139.982 2836 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.60 % Favored : 87.83 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.17), residues: 2482 helix: -0.68 (0.13), residues: 1402 sheet: -2.78 (0.53), residues: 74 loop : -2.66 (0.20), residues: 1006 *********************** 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 424 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 399 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 406 average time/residue: 0.2956 time to fit residues: 192.0951 Evaluate side-chains 403 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 387 time to evaluate : 2.271 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2113 time to fit residues: 9.5077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 9.9990 chunk 143 optimal weight: 0.0670 chunk 111 optimal weight: 0.3980 chunk 163 optimal weight: 0.6980 chunk 247 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 387 GLN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN D 222 ASN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 20824 Z= 0.226 Angle : 1.033 25.915 28272 Z= 0.452 Chirality : 0.092 2.314 3218 Planarity : 0.005 0.072 3512 Dihedral : 8.452 140.103 2836 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.56 % Favored : 87.87 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.16), residues: 2482 helix: -0.64 (0.13), residues: 1390 sheet: -2.71 (0.54), residues: 74 loop : -2.61 (0.20), residues: 1018 ********************** 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 403 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 397 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 398 average time/residue: 0.2899 time to fit residues: 186.1823 Evaluate side-chains 394 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 389 time to evaluate : 2.288 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2104 time to fit residues: 5.1954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.0670 chunk 60 optimal weight: 4.9990 chunk 181 optimal weight: 8.9990 chunk 29 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 173 optimal weight: 0.7980 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.185724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.132441 restraints weight = 56491.866| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 4.43 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 20824 Z= 0.227 Angle : 1.030 25.764 28272 Z= 0.448 Chirality : 0.092 2.307 3218 Planarity : 0.005 0.070 3512 Dihedral : 8.372 140.297 2836 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.52 % Favored : 87.91 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.17), residues: 2482 helix: -0.64 (0.13), residues: 1394 sheet: -2.64 (0.55), residues: 74 loop : -2.53 (0.20), residues: 1014 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4558.73 seconds wall clock time: 84 minutes 0.49 seconds (5040.49 seconds total)