Starting phenix.real_space_refine on Mon Mar 25 00:21:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdp_9103/03_2024/6mdp_9103_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdp_9103/03_2024/6mdp_9103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdp_9103/03_2024/6mdp_9103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdp_9103/03_2024/6mdp_9103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdp_9103/03_2024/6mdp_9103_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdp_9103/03_2024/6mdp_9103_trim_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 S 124 5.16 5 C 14117 2.51 5 N 3901 2.21 5 O 4260 1.98 5 H 22777 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 303": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 413": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 455": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 691": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 727": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 734": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 413": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 415": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 455": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 516": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 727": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 734": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 238": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 303": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 648": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 280": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 446": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 516": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 725": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 727": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 617": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 725": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 734": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45210 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 8088 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 22, 'TRANS': 488} Chain breaks: 1 Chain: "B" Number of atoms: 8167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 8167 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 23, 'TRANS': 492} Chain breaks: 1 Chain: "C" Number of atoms: 8337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 8337 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 23, 'TRANS': 503} Chain breaks: 1 Chain: "D" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 8314 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 23, 'TRANS': 502} Chain breaks: 1 Chain: "E" Number of atoms: 7788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 7788 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 20, 'TRANS': 471} Chain breaks: 2 Chain: "F" Number of atoms: 3906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3906 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 12, 'TRANS': 230} Chain: "H" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 277 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.51, per 1000 atoms: 0.41 Number of scatterers: 45210 At special positions: 0 Unit cell: (144.1, 141.48, 121.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 31 15.00 O 4260 8.00 N 3901 7.00 C 14117 6.00 H 22777 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 32.78 Conformation dependent library (CDL) restraints added in 4.5 seconds 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5238 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 123 helices and 12 sheets defined 43.1% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.11 Creating SS restraints... Processing helix chain 'A' and resid 227 through 238 removed outlier: 4.160A pdb=" N ALA A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N SER A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.603A pdb=" N ALA A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 290 No H-bonds generated for 'chain 'A' and resid 287 through 290' Processing helix chain 'A' and resid 297 through 300 No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 303 through 315 removed outlier: 4.117A pdb=" N ASP A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 358 removed outlier: 3.609A pdb=" N SER A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 384 No H-bonds generated for 'chain 'A' and resid 381 through 384' Processing helix chain 'A' and resid 400 through 417 removed outlier: 4.210A pdb=" N MET A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 432 Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 480 through 484 Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 512 through 529 removed outlier: 3.748A pdb=" N GLN A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 558 removed outlier: 4.493A pdb=" N ALA A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS A 555 " --> pdb=" O ALA A 551 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 594 removed outlier: 3.768A pdb=" N GLN A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 589 " --> pdb=" O MET A 585 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 608 No H-bonds generated for 'chain 'A' and resid 605 through 608' Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 650 through 654 Processing helix chain 'A' and resid 673 through 682 Processing helix chain 'A' and resid 688 through 699 removed outlier: 3.977A pdb=" N GLN A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLN A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 718 removed outlier: 3.991A pdb=" N GLU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 4.153A pdb=" N VAL A 726 " --> pdb=" O PRO A 722 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARG A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A 728 " --> pdb=" O TYR A 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 234 removed outlier: 4.002A pdb=" N ARG B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 266 through 275 removed outlier: 4.503A pdb=" N GLY B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 290 removed outlier: 4.137A pdb=" N ILE B 290 " --> pdb=" O GLY B 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 287 through 290' Processing helix chain 'B' and resid 297 through 316 removed outlier: 3.728A pdb=" N ILE B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 357 Processing helix chain 'B' and resid 381 through 384 No H-bonds generated for 'chain 'B' and resid 381 through 384' Processing helix chain 'B' and resid 400 through 415 removed outlier: 3.922A pdb=" N THR B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG B 413 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N MET B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 432 Processing helix chain 'B' and resid 440 through 456 Processing helix chain 'B' and resid 481 through 488 removed outlier: 4.682A pdb=" N ASP B 487 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 529 removed outlier: 3.757A pdb=" N THR B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 578 through 594 removed outlier: 4.440A pdb=" N ILE B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 589 " --> pdb=" O MET B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 608 No H-bonds generated for 'chain 'B' and resid 605 through 608' Processing helix chain 'B' and resid 620 through 630 Processing helix chain 'B' and resid 650 through 655 Processing helix chain 'B' and resid 657 through 660 No H-bonds generated for 'chain 'B' and resid 657 through 660' Processing helix chain 'B' and resid 673 through 683 removed outlier: 3.891A pdb=" N GLU B 678 " --> pdb=" O GLU B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 697 removed outlier: 3.681A pdb=" N THR B 693 " --> pdb=" O LYS B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 718 removed outlier: 4.122A pdb=" N MET B 712 " --> pdb=" O LYS B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 735 removed outlier: 3.859A pdb=" N GLU B 735 " --> pdb=" O ALA B 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 234 removed outlier: 3.907A pdb=" N ILE C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 266 through 272 Processing helix chain 'C' and resid 288 through 290 No H-bonds generated for 'chain 'C' and resid 288 through 290' Processing helix chain 'C' and resid 297 through 308 removed outlier: 4.020A pdb=" N ILE C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU C 305 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE C 306 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 315 Processing helix chain 'C' and resid 346 through 358 removed outlier: 3.595A pdb=" N LEU C 355 " --> pdb=" O ASN C 352 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE C 358 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 384 No H-bonds generated for 'chain 'C' and resid 381 through 384' Processing helix chain 'C' and resid 402 through 416 removed outlier: 3.763A pdb=" N HIS C 410 " --> pdb=" O ILE C 406 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N MET C 414 " --> pdb=" O HIS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 430 No H-bonds generated for 'chain 'C' and resid 427 through 430' Processing helix chain 'C' and resid 438 through 457 removed outlier: 3.831A pdb=" N GLY C 443 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 444 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN C 449 " --> pdb=" O ARG C 446 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG C 455 " --> pdb=" O ALA C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 485 Processing helix chain 'C' and resid 512 through 529 removed outlier: 4.018A pdb=" N GLN C 527 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR C 528 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 559 Processing helix chain 'C' and resid 578 through 592 Processing helix chain 'C' and resid 605 through 608 No H-bonds generated for 'chain 'C' and resid 605 through 608' Processing helix chain 'C' and resid 620 through 631 removed outlier: 3.529A pdb=" N LEU C 630 " --> pdb=" O LEU C 626 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 631 " --> pdb=" O LEU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 655 Processing helix chain 'C' and resid 673 through 683 removed outlier: 3.902A pdb=" N GLU C 678 " --> pdb=" O GLU C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 699 removed outlier: 3.845A pdb=" N GLN C 696 " --> pdb=" O THR C 692 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLN C 697 " --> pdb=" O THR C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 717 removed outlier: 3.711A pdb=" N MET C 712 " --> pdb=" O LYS C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 736 Processing helix chain 'D' and resid 225 through 234 Processing helix chain 'D' and resid 242 through 248 Processing helix chain 'D' and resid 266 through 276 removed outlier: 4.351A pdb=" N GLY D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 314 removed outlier: 4.722A pdb=" N ILE D 302 " --> pdb=" O SER D 298 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG D 303 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 333 No H-bonds generated for 'chain 'D' and resid 330 through 333' Processing helix chain 'D' and resid 346 through 348 No H-bonds generated for 'chain 'D' and resid 346 through 348' Processing helix chain 'D' and resid 351 through 359 Processing helix chain 'D' and resid 376 through 378 No H-bonds generated for 'chain 'D' and resid 376 through 378' Processing helix chain 'D' and resid 400 through 416 removed outlier: 4.451A pdb=" N ARG D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N MET D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 432 Processing helix chain 'D' and resid 439 through 457 removed outlier: 3.998A pdb=" N VAL D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG D 455 " --> pdb=" O THR D 451 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N HIS D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 488 removed outlier: 4.206A pdb=" N ILE D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 530 Processing helix chain 'D' and resid 549 through 560 removed outlier: 4.007A pdb=" N ILE D 556 " --> pdb=" O LEU D 552 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA D 557 " --> pdb=" O ALA D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 594 removed outlier: 3.805A pdb=" N MET D 585 " --> pdb=" O LYS D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 608 No H-bonds generated for 'chain 'D' and resid 605 through 608' Processing helix chain 'D' and resid 620 through 631 Processing helix chain 'D' and resid 650 through 655 Processing helix chain 'D' and resid 673 through 681 removed outlier: 4.458A pdb=" N GLU D 678 " --> pdb=" O GLU D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 701 removed outlier: 4.034A pdb=" N GLN D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN D 697 " --> pdb=" O THR D 693 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY D 700 " --> pdb=" O GLN D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 720 removed outlier: 3.824A pdb=" N GLU D 715 " --> pdb=" O LEU D 711 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET D 720 " --> pdb=" O MET D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 733 removed outlier: 3.817A pdb=" N ALA D 731 " --> pdb=" O ARG D 727 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 229 Processing helix chain 'E' and resid 266 through 276 removed outlier: 3.911A pdb=" N ALA E 270 " --> pdb=" O LYS E 266 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS E 275 " --> pdb=" O ARG E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 290 No H-bonds generated for 'chain 'E' and resid 288 through 290' Processing helix chain 'E' and resid 297 through 306 removed outlier: 3.597A pdb=" N ILE E 302 " --> pdb=" O SER E 298 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE E 306 " --> pdb=" O ILE E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 317 No H-bonds generated for 'chain 'E' and resid 315 through 317' Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 352 through 359 removed outlier: 4.250A pdb=" N ILE E 358 " --> pdb=" O LEU E 354 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP E 359 " --> pdb=" O LEU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 402 through 416 removed outlier: 3.794A pdb=" N ILE E 409 " --> pdb=" O GLN E 405 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N HIS E 410 " --> pdb=" O ILE E 406 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG E 413 " --> pdb=" O ILE E 409 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N MET E 414 " --> pdb=" O HIS E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 430 Processing helix chain 'E' and resid 440 through 453 removed outlier: 3.657A pdb=" N GLY E 443 " --> pdb=" O GLU E 440 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LEU E 444 " --> pdb=" O LEU E 441 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR E 451 " --> pdb=" O ALA E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 488 Processing helix chain 'E' and resid 512 through 529 Processing helix chain 'E' and resid 550 through 558 Processing helix chain 'E' and resid 578 through 594 removed outlier: 3.735A pdb=" N CYS E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 608 No H-bonds generated for 'chain 'E' and resid 605 through 608' Processing helix chain 'E' and resid 620 through 629 removed outlier: 3.600A pdb=" N VAL E 628 " --> pdb=" O GLN E 624 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 655 Processing helix chain 'E' and resid 657 through 660 No H-bonds generated for 'chain 'E' and resid 657 through 660' Processing helix chain 'E' and resid 673 through 683 Processing helix chain 'E' and resid 688 through 697 removed outlier: 3.703A pdb=" N GLN E 696 " --> pdb=" O THR E 692 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLN E 697 " --> pdb=" O THR E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 707 through 719 removed outlier: 4.231A pdb=" N GLU E 715 " --> pdb=" O LEU E 711 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N MET E 716 " --> pdb=" O MET E 712 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER E 717 " --> pdb=" O LEU E 713 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 735 Processing helix chain 'F' and resid 512 through 529 removed outlier: 3.823A pdb=" N ASP F 520 " --> pdb=" O ARG F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 560 Processing helix chain 'F' and resid 578 through 592 removed outlier: 3.941A pdb=" N PHE F 589 " --> pdb=" O MET F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 609 Processing helix chain 'F' and resid 620 through 629 Processing helix chain 'F' and resid 650 through 654 Processing helix chain 'F' and resid 673 through 683 Processing helix chain 'F' and resid 688 through 698 removed outlier: 4.112A pdb=" N THR F 693 " --> pdb=" O LYS F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 707 through 716 removed outlier: 3.750A pdb=" N MET F 712 " --> pdb=" O LYS F 708 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU F 715 " --> pdb=" O LEU F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 724 No H-bonds generated for 'chain 'F' and resid 721 through 724' Processing helix chain 'F' and resid 726 through 737 removed outlier: 3.890A pdb=" N GLU F 735 " --> pdb=" O ALA F 731 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU F 736 " --> pdb=" O LEU F 732 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 391 through 395 removed outlier: 6.214A pdb=" N VAL A 369 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU A 258 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY A 371 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N GLY A 260 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N THR A 373 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE A 325 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N MET A 372 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE A 327 " --> pdb=" O MET A 372 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS A 283 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 536 through 540 removed outlier: 6.897A pdb=" N LEU A 640 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N VAL A 539 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE A 642 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE A 564 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VAL A 601 " --> pdb=" O PHE A 564 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS A 566 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ASP A 603 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N CYS A 568 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 256 through 259 Processing sheet with id= D, first strand: chain 'B' and resid 540 through 542 Processing sheet with id= E, first strand: chain 'C' and resid 255 through 259 removed outlier: 6.070A pdb=" N VAL C 369 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU C 258 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY C 371 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 536 through 540 removed outlier: 6.683A pdb=" N LEU C 640 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N VAL C 539 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE C 642 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 541 through 543 removed outlier: 6.134A pdb=" N ILE C 665 " --> pdb=" O GLU C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 256 through 258 removed outlier: 6.480A pdb=" N VAL D 391 " --> pdb=" O LEU D 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'D' and resid 663 through 667 removed outlier: 3.801A pdb=" N LEU D 540 " --> pdb=" O THR D 663 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE D 642 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N LEU D 541 " --> pdb=" O ILE D 642 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY D 644 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLY D 543 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR D 646 " --> pdb=" O GLY D 543 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE D 564 " --> pdb=" O CYS D 599 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL D 601 " --> pdb=" O PHE D 564 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS D 566 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP D 603 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N CYS D 568 " --> pdb=" O ASP D 603 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 324 through 328 removed outlier: 6.531A pdb=" N LEU E 368 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N PHE E 327 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE E 370 " --> pdb=" O PHE E 327 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 665 through 667 removed outlier: 6.489A pdb=" N LEU E 640 " --> pdb=" O VAL E 537 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL E 539 " --> pdb=" O LEU E 640 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE E 642 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU E 541 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY E 644 " --> pdb=" O LEU E 541 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N GLY E 543 " --> pdb=" O GLY E 644 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR E 646 " --> pdb=" O GLY E 543 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE E 564 " --> pdb=" O CYS E 599 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL E 601 " --> pdb=" O PHE E 564 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS E 566 " --> pdb=" O VAL E 601 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 538 through 540 removed outlier: 8.899A pdb=" N VAL F 539 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE F 642 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE F 564 " --> pdb=" O CYS F 599 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL F 601 " --> pdb=" O PHE F 564 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS F 566 " --> pdb=" O VAL F 601 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ASP F 603 " --> pdb=" O LYS F 566 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N CYS F 568 " --> pdb=" O ASP F 603 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1932 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: 18.04 Time building geometry restraints manager: 34.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 22745 1.03 - 1.22: 49 1.22 - 1.42: 8815 1.42 - 1.62: 13733 1.62 - 1.82: 216 Bond restraints: 45558 Sorted by residual: bond pdb=" C4 ATP F 801 " pdb=" C5 ATP F 801 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.29e+01 bond pdb=" C4 ATP A 802 " pdb=" C5 ATP A 802 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.10e+01 bond pdb=" C4 ATP D 802 " pdb=" C5 ATP D 802 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.81e+01 bond pdb=" C4 ATP B 801 " pdb=" C5 ATP B 801 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.71e+01 bond pdb=" C4 ATP B 802 " pdb=" C5 ATP B 802 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.58e+01 ... (remaining 45553 not shown) Histogram of bond angle deviations from ideal: 76.46 - 88.78: 89 88.78 - 101.10: 76 101.10 - 113.42: 56528 113.42 - 125.74: 25610 125.74 - 138.07: 580 Bond angle restraints: 82883 Sorted by residual: angle pdb=" PB ATP B 802 " pdb=" O3B ATP B 802 " pdb=" PG ATP B 802 " ideal model delta sigma weight residual 139.87 115.29 24.58 1.00e+00 1.00e+00 6.04e+02 angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 115.95 23.92 1.00e+00 1.00e+00 5.72e+02 angle pdb=" PB ATP F 801 " pdb=" O3B ATP F 801 " pdb=" PG ATP F 801 " ideal model delta sigma weight residual 139.87 116.11 23.76 1.00e+00 1.00e+00 5.65e+02 angle pdb=" PA ATP F 801 " pdb=" O3A ATP F 801 " pdb=" PB ATP F 801 " ideal model delta sigma weight residual 136.83 114.54 22.29 1.00e+00 1.00e+00 4.97e+02 angle pdb=" PB ATP C 802 " pdb=" O3B ATP C 802 " pdb=" PG ATP C 802 " ideal model delta sigma weight residual 139.87 117.62 22.25 1.00e+00 1.00e+00 4.95e+02 ... (remaining 82878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.46: 20508 32.46 - 64.93: 612 64.93 - 97.39: 44 97.39 - 129.86: 2 129.86 - 162.32: 2 Dihedral angle restraints: 21168 sinusoidal: 12241 harmonic: 8927 Sorted by residual: dihedral pdb=" C5' ADP E 802 " pdb=" O5' ADP E 802 " pdb=" PA ADP E 802 " pdb=" O2A ADP E 802 " ideal model delta sinusoidal sigma weight residual -60.00 102.33 -162.32 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" O2A ADP E 802 " pdb=" O3A ADP E 802 " pdb=" PA ADP E 802 " pdb=" PB ADP E 802 " ideal model delta sinusoidal sigma weight residual -60.00 84.48 -144.48 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" O1B ADP E 802 " pdb=" O3A ADP E 802 " pdb=" PB ADP E 802 " pdb=" PA ADP E 802 " ideal model delta sinusoidal sigma weight residual -60.00 56.55 -116.55 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 21165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.417: 3490 0.417 - 0.835: 0 0.835 - 1.252: 0 1.252 - 1.669: 11 1.669 - 2.087: 17 Chirality restraints: 3518 Sorted by residual: chirality pdb=" CG LEU B 552 " pdb=" CB LEU B 552 " pdb=" CD1 LEU B 552 " pdb=" CD2 LEU B 552 " both_signs ideal model delta sigma weight residual False -2.59 -0.50 -2.09 2.00e-01 2.50e+01 1.09e+02 chirality pdb=" CG LEU A 419 " pdb=" CB LEU A 419 " pdb=" CD1 LEU A 419 " pdb=" CD2 LEU A 419 " both_signs ideal model delta sigma weight residual False -2.59 -0.51 -2.08 2.00e-01 2.50e+01 1.08e+02 chirality pdb=" CG LEU E 384 " pdb=" CB LEU E 384 " pdb=" CD1 LEU E 384 " pdb=" CD2 LEU E 384 " both_signs ideal model delta sigma weight residual False -2.59 -0.58 -2.01 2.00e-01 2.50e+01 1.01e+02 ... (remaining 3515 not shown) Planarity restraints: 6616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 486 " 0.045 2.00e-02 2.50e+03 6.49e-02 6.31e+01 pdb=" CG ASN B 486 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 486 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN B 486 " -0.110 2.00e-02 2.50e+03 pdb="HD21 ASN B 486 " -0.012 2.00e-02 2.50e+03 pdb="HD22 ASN B 486 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 278 " -0.040 2.00e-02 2.50e+03 5.65e-02 4.79e+01 pdb=" CG ASN D 278 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN D 278 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN D 278 " 0.092 2.00e-02 2.50e+03 pdb="HD21 ASN D 278 " 0.013 2.00e-02 2.50e+03 pdb="HD22 ASN D 278 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 418 " -0.046 2.00e-02 2.50e+03 5.52e-02 4.57e+01 pdb=" CD GLN D 418 " 0.045 2.00e-02 2.50e+03 pdb=" OE1 GLN D 418 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN D 418 " 0.084 2.00e-02 2.50e+03 pdb="HE21 GLN D 418 " 0.003 2.00e-02 2.50e+03 pdb="HE22 GLN D 418 " -0.084 2.00e-02 2.50e+03 ... (remaining 6613 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 4406 2.23 - 2.82: 100631 2.82 - 3.41: 116332 3.41 - 4.01: 153078 4.01 - 4.60: 238627 Nonbonded interactions: 613074 Sorted by model distance: nonbonded pdb=" O SER A 531 " pdb=" HZ2 LYS A 639 " model vdw 1.633 1.850 nonbonded pdb=" HE2 LYS D 702 " pdb=" HZ3 LYS D 702 " model vdw 1.636 1.816 nonbonded pdb=" OD2 ASP E 331 " pdb="HH11 ARG E 375 " model vdw 1.642 1.850 nonbonded pdb=" O THR D 692 " pdb="HE22 GLN D 696 " model vdw 1.672 1.850 nonbonded pdb=" O PRO B 211 " pdb=" H ASN B 278 " model vdw 1.672 1.850 ... (remaining 613069 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 216 through 235 or resid 252 through 262 or (resid 263 and \ (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 264 t \ hrough 344 or (resid 345 and (name N or name CA or name C or name O or name H or \ name HA2)) or resid 346 through 384 or (resid 385 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG \ 3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH22)) or \ resid 386 through 457 or resid 476 through 606 or (resid 607 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name NE or name CZ \ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or r \ esid 608 through 738)) selection = (chain 'B' and (resid 216 through 235 or resid 252 through 262 or (resid 263 and \ (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 264 t \ hrough 344 or (resid 345 and (name N or name CA or name C or name O or name H or \ name HA2)) or resid 346 through 384 or (resid 385 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG \ 3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH22)) or \ resid 386 through 457 or resid 476 through 606 or (resid 607 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name NE or name CZ \ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 \ or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH12)) or r \ esid 608 through 738)) selection = (chain 'C' and (resid 216 through 235 or resid 252 through 262 or (resid 263 and \ (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 264 t \ hrough 384 or (resid 385 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or \ name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 \ or name HE or name HH11 or name HH12 or name HH22)) or resid 386 through 457 or \ resid 476 through 738)) selection = (chain 'D' and (resid 216 through 235 or resid 252 through 262 or (resid 263 and \ (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 264 t \ hrough 344 or (resid 345 and (name N or name CA or name C or name O or name H or \ name HA2)) or resid 346 through 457 or resid 476 through 606 or (resid 607 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name H \ B3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or na \ me HH12)) or resid 608 through 738)) selection = (chain 'E' and (resid 216 through 344 or (resid 345 and (name N or name CA or na \ me C or name O or name H or name HA2)) or resid 346 through 384 or (resid 385 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e NE or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name \ HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or \ name HH12 or name HH22)) or resid 386 through 457 or resid 476 through 606 or (r \ esid 607 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name \ HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or na \ me HH11 or name HH12)) or resid 608 through 738)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.610 Extract box with map and model: 4.990 Check model and map are aligned: 0.610 Set scattering table: 0.400 Process input model: 132.540 Find NCS groups from input model: 2.940 Set up NCS constraints: 0.150 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 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 : 0.009 0.091 22781 Z= 0.591 Angle : 1.424 26.166 30766 Z= 0.882 Chirality : 0.167 2.087 3518 Planarity : 0.007 0.072 3921 Dihedral : 13.116 162.323 9003 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.35 % Favored : 97.51 % Rotamer: Outliers : 0.33 % Allowed : 7.28 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.13), residues: 2806 helix: -2.28 (0.12), residues: 1258 sheet: -2.40 (0.25), residues: 305 loop : -2.32 (0.16), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 704 HIS 0.043 0.003 HIS A 417 PHE 0.043 0.004 PHE D 231 TYR 0.027 0.003 TYR A 502 ARG 0.019 0.001 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 195 time to evaluate : 3.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 MET cc_start: 0.5494 (pp-130) cc_final: 0.4188 (pp-130) REVERT: C 340 MET cc_start: 0.1768 (mtm) cc_final: 0.0902 (mmt) REVERT: C 573 MET cc_start: 0.4995 (ptp) cc_final: 0.4686 (ptt) outliers start: 8 outliers final: 2 residues processed: 203 average time/residue: 0.9142 time to fit residues: 279.1056 Evaluate side-chains 139 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 566 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 254 optimal weight: 6.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 363 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN B 214 ASN ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN D 247 GLN D 278 ASN D 301 ASN D 374 ASN D 561 ASN ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 ASN E 474 GLN E 486 ASN ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 620 ASN ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 527 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22781 Z= 0.262 Angle : 0.804 25.709 30766 Z= 0.394 Chirality : 0.150 1.776 3518 Planarity : 0.004 0.065 3921 Dihedral : 11.769 165.712 3345 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.63 % Favored : 94.30 % Rotamer: Outliers : 0.87 % Allowed : 10.33 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.14), residues: 2806 helix: -1.27 (0.13), residues: 1273 sheet: -2.02 (0.26), residues: 320 loop : -2.17 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 704 HIS 0.006 0.001 HIS E 410 PHE 0.017 0.002 PHE D 231 TYR 0.014 0.002 TYR E 499 ARG 0.009 0.001 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 340 MET cc_start: 0.2275 (mtm) cc_final: 0.1418 (mmt) REVERT: D 655 MET cc_start: 0.5946 (ptp) cc_final: 0.5742 (mtm) outliers start: 21 outliers final: 13 residues processed: 151 average time/residue: 0.8081 time to fit residues: 189.0493 Evaluate side-chains 143 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 3.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain F residue 645 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 211 optimal weight: 0.4980 chunk 173 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 254 optimal weight: 8.9990 chunk 275 optimal weight: 9.9990 chunk 226 optimal weight: 20.0000 chunk 252 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN C 363 GLN D 530 ASN ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 675 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22781 Z= 0.287 Angle : 0.784 25.659 30766 Z= 0.384 Chirality : 0.150 1.786 3518 Planarity : 0.004 0.052 3921 Dihedral : 11.011 160.164 3341 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.81 % Favored : 93.12 % Rotamer: Outliers : 0.74 % Allowed : 11.29 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.15), residues: 2806 helix: -0.81 (0.14), residues: 1271 sheet: -1.76 (0.27), residues: 329 loop : -2.13 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 213 HIS 0.006 0.001 HIS E 410 PHE 0.017 0.002 PHE D 492 TYR 0.013 0.002 TYR E 499 ARG 0.007 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 420 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6224 (pp) REVERT: C 340 MET cc_start: 0.1366 (mtm) cc_final: 0.0940 (mmp) REVERT: D 655 MET cc_start: 0.6087 (ptp) cc_final: 0.5864 (mtm) outliers start: 18 outliers final: 12 residues processed: 141 average time/residue: 0.8328 time to fit residues: 182.2158 Evaluate side-chains 133 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 3.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 414 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 121 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 255 optimal weight: 9.9990 chunk 270 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22781 Z= 0.189 Angle : 0.733 26.083 30766 Z= 0.346 Chirality : 0.150 1.745 3518 Planarity : 0.004 0.046 3921 Dihedral : 10.606 175.105 3341 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.09 % Favored : 93.87 % Rotamer: Outliers : 0.83 % Allowed : 12.15 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.15), residues: 2806 helix: -0.37 (0.14), residues: 1274 sheet: -1.37 (0.28), residues: 307 loop : -1.95 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 213 HIS 0.004 0.001 HIS D 417 PHE 0.013 0.001 PHE D 327 TYR 0.015 0.001 TYR E 499 ARG 0.006 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.6723 (tpp) cc_final: 0.6376 (tpp) REVERT: B 420 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6254 (pp) REVERT: C 340 MET cc_start: 0.1496 (mtm) cc_final: 0.1067 (mmp) REVERT: C 414 MET cc_start: 0.6240 (mmp) cc_final: 0.5477 (mmp) REVERT: D 655 MET cc_start: 0.6210 (ptp) cc_final: 0.5985 (mtm) REVERT: F 585 MET cc_start: 0.6732 (ppp) cc_final: 0.5989 (ppp) REVERT: H 1 MET cc_start: 0.7269 (tpp) cc_final: 0.7064 (tpt) outliers start: 20 outliers final: 13 residues processed: 141 average time/residue: 0.7939 time to fit residues: 175.4363 Evaluate side-chains 137 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 505 ASN Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain F residue 645 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 8.9990 chunk 153 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 201 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 230 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 527 GLN ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22781 Z= 0.224 Angle : 0.734 25.765 30766 Z= 0.350 Chirality : 0.149 1.755 3518 Planarity : 0.004 0.041 3921 Dihedral : 10.194 149.087 3341 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.31 % Favored : 92.66 % Rotamer: Outliers : 0.95 % Allowed : 12.44 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.15), residues: 2806 helix: -0.30 (0.14), residues: 1290 sheet: -1.34 (0.28), residues: 313 loop : -1.97 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 213 HIS 0.005 0.001 HIS D 417 PHE 0.017 0.001 PHE D 327 TYR 0.012 0.001 TYR E 499 ARG 0.005 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 3.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 420 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6431 (pp) REVERT: C 340 MET cc_start: 0.1519 (mtm) cc_final: 0.1013 (mmp) REVERT: D 655 MET cc_start: 0.6244 (ptp) cc_final: 0.6038 (mtm) outliers start: 23 outliers final: 17 residues processed: 142 average time/residue: 0.8271 time to fit residues: 182.7460 Evaluate side-chains 141 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 724 TYR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 505 ASN Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 561 ASN Chi-restraints excluded: chain F residue 645 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 2.9990 chunk 243 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 270 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22781 Z= 0.186 Angle : 0.723 26.002 30766 Z= 0.338 Chirality : 0.149 1.753 3518 Planarity : 0.003 0.039 3921 Dihedral : 10.007 137.724 3341 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.49 % Favored : 93.48 % Rotamer: Outliers : 0.99 % Allowed : 12.65 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.16), residues: 2806 helix: -0.08 (0.15), residues: 1285 sheet: -1.08 (0.29), residues: 302 loop : -1.88 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 213 HIS 0.004 0.001 HIS D 417 PHE 0.015 0.001 PHE D 327 TYR 0.014 0.001 TYR D 294 ARG 0.005 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 3.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 420 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6424 (pp) REVERT: C 340 MET cc_start: 0.2009 (mtm) cc_final: 0.1449 (mmp) REVERT: D 655 MET cc_start: 0.6210 (ptp) cc_final: 0.5998 (mtm) outliers start: 24 outliers final: 16 residues processed: 144 average time/residue: 0.7726 time to fit residues: 175.6425 Evaluate side-chains 139 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 724 TYR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 561 ASN Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 645 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 6.9990 chunk 30 optimal weight: 0.0670 chunk 154 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 269 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22781 Z= 0.172 Angle : 0.715 26.093 30766 Z= 0.332 Chirality : 0.149 1.750 3518 Planarity : 0.003 0.038 3921 Dihedral : 9.786 132.616 3341 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.59 % Favored : 93.37 % Rotamer: Outliers : 0.79 % Allowed : 13.15 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.16), residues: 2806 helix: 0.15 (0.15), residues: 1280 sheet: -0.95 (0.30), residues: 300 loop : -1.83 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 213 HIS 0.004 0.001 HIS D 408 PHE 0.015 0.001 PHE D 327 TYR 0.007 0.001 TYR A 502 ARG 0.004 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 3.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 420 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6229 (pp) REVERT: C 340 MET cc_start: 0.1916 (mtm) cc_final: 0.1300 (mmp) REVERT: D 655 MET cc_start: 0.6185 (ptp) cc_final: 0.5961 (mtm) outliers start: 19 outliers final: 15 residues processed: 141 average time/residue: 0.7709 time to fit residues: 170.7229 Evaluate side-chains 138 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 3.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 561 ASN Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 645 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 25 optimal weight: 0.2980 chunk 212 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22781 Z= 0.193 Angle : 0.719 25.773 30766 Z= 0.337 Chirality : 0.149 1.752 3518 Planarity : 0.003 0.037 3921 Dihedral : 9.597 126.343 3341 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.79 % Allowed : 13.10 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.16), residues: 2806 helix: 0.12 (0.15), residues: 1299 sheet: -0.93 (0.30), residues: 302 loop : -1.82 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 213 HIS 0.004 0.001 HIS D 417 PHE 0.011 0.001 PHE D 492 TYR 0.007 0.001 TYR A 502 ARG 0.004 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 3.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 420 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6288 (pp) REVERT: C 340 MET cc_start: 0.2429 (mtm) cc_final: 0.2020 (mmp) REVERT: D 655 MET cc_start: 0.6230 (ptp) cc_final: 0.6003 (mtm) outliers start: 19 outliers final: 17 residues processed: 139 average time/residue: 0.7990 time to fit residues: 173.7473 Evaluate side-chains 138 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 3.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 561 ASN Chi-restraints excluded: chain F residue 645 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 6.9990 chunk 258 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 251 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 197 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 237 optimal weight: 8.9990 chunk 250 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN D 675 GLN ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22781 Z= 0.168 Angle : 0.719 26.099 30766 Z= 0.331 Chirality : 0.149 1.752 3518 Planarity : 0.003 0.037 3921 Dihedral : 9.453 119.801 3341 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.70 % Allowed : 13.02 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.16), residues: 2806 helix: 0.31 (0.15), residues: 1303 sheet: -0.71 (0.31), residues: 293 loop : -1.75 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 213 HIS 0.004 0.001 HIS D 408 PHE 0.031 0.001 PHE D 327 TYR 0.007 0.001 TYR B 259 ARG 0.005 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 3.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 420 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6359 (pp) REVERT: C 340 MET cc_start: 0.2377 (mtm) cc_final: 0.2005 (mmp) REVERT: D 655 MET cc_start: 0.6178 (ptp) cc_final: 0.5934 (mtm) outliers start: 17 outliers final: 16 residues processed: 140 average time/residue: 0.8504 time to fit residues: 188.6185 Evaluate side-chains 139 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 3.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 645 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 6.9990 chunk 265 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 278 optimal weight: 10.0000 chunk 256 optimal weight: 0.0870 chunk 222 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22781 Z= 0.260 Angle : 0.753 24.992 30766 Z= 0.360 Chirality : 0.150 1.785 3518 Planarity : 0.004 0.037 3921 Dihedral : 9.460 126.580 3341 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.87 % Allowed : 13.15 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.16), residues: 2806 helix: -0.01 (0.14), residues: 1299 sheet: -1.13 (0.29), residues: 316 loop : -1.88 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 213 HIS 0.006 0.001 HIS D 417 PHE 0.012 0.002 PHE A 227 TYR 0.011 0.001 TYR D 611 ARG 0.006 0.001 ARG D 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5612 Ramachandran restraints generated. 2806 Oldfield, 0 Emsley, 2806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 420 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5791 (pp) REVERT: C 340 MET cc_start: 0.2629 (mtm) cc_final: 0.2100 (mmp) REVERT: D 655 MET cc_start: 0.6304 (ptp) cc_final: 0.6097 (mtm) outliers start: 21 outliers final: 18 residues processed: 137 average time/residue: 0.8096 time to fit residues: 173.7800 Evaluate side-chains 136 residues out of total 2419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain B residue 213 TRP Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 504 MET Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 561 ASN Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 645 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 204 optimal weight: 0.2980 chunk 32 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 222 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.031613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.024228 restraints weight = 625884.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.025500 restraints weight = 319001.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.026463 restraints weight = 198803.426| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22781 Z= 0.170 Angle : 0.726 26.314 30766 Z= 0.334 Chirality : 0.149 1.737 3518 Planarity : 0.003 0.035 3921 Dihedral : 9.237 123.265 3341 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.58 % Allowed : 13.44 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2806 helix: 0.40 (0.15), residues: 1306 sheet: -0.63 (0.31), residues: 290 loop : -1.76 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 213 HIS 0.005 0.001 HIS D 408 PHE 0.013 0.001 PHE E 306 TYR 0.009 0.001 TYR D 499 ARG 0.006 0.000 ARG D 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6223.10 seconds wall clock time: 113 minutes 41.43 seconds (6821.43 seconds total)