Starting phenix.real_space_refine on Mon Mar 25 00:53:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdo_9102/03_2024/6mdo_9102_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdo_9102/03_2024/6mdo_9102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdo_9102/03_2024/6mdo_9102.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdo_9102/03_2024/6mdo_9102.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdo_9102/03_2024/6mdo_9102_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdo_9102/03_2024/6mdo_9102_trim_updated.pdb" } resolution = 3.9 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= 0.003 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 125 5.16 5 C 14171 2.51 5 N 3917 2.21 5 O 4271 1.98 5 H 22858 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 315": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 388": not complete - not flipped Residue "A ARG 403": "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 PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 617": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 734": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 413": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 415": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B LEU 420": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23" Residue "B ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 691": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 734": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 455": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 516": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 280": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 303": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 238": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 280": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 446": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 477": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 725": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 533": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 727": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45373 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 8082 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 22, 'TRANS': 488} Chain breaks: 1 Chain: "B" Number of atoms: 8203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 8203 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 23, 'TRANS': 495} Chain breaks: 1 Chain: "C" Number of atoms: 8244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 8244 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 23, 'TRANS': 497} Chain breaks: 1 Chain: "D" Number of atoms: 8308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 8308 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 23, 'TRANS': 501} Chain breaks: 1 Chain: "E" Number of atoms: 8059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 8059 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 20, 'TRANS': 488} Chain breaks: 2 Chain: "F" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3874 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "H" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 270 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: 18.93, per 1000 atoms: 0.42 Number of scatterers: 45373 At special positions: 0 Unit cell: (148.03, 131, 117.9, 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 125 16.00 P 31 15.00 O 4271 8.00 N 3917 7.00 C 14171 6.00 H 22858 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: 34.59 Conformation dependent library (CDL) restraints added in 4.6 seconds 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5260 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 13 sheets defined 44.2% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.79 Creating SS restraints... Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 242 through 248 removed outlier: 4.510A pdb=" N GLN A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.616A pdb=" N ARG A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 295 through 316 removed outlier: 4.023A pdb=" N GLU A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 358 Processing helix chain 'A' and resid 400 through 417 removed outlier: 4.654A pdb=" N ARG A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N MET A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 432 removed outlier: 3.906A pdb=" N VAL A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 removed outlier: 3.869A pdb=" N GLU A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET A 453 " --> pdb=" O GLN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 485 No H-bonds generated for 'chain 'A' and resid 482 through 485' Processing helix chain 'A' and resid 499 through 502 No H-bonds generated for 'chain 'A' and resid 499 through 502' Processing helix chain 'A' and resid 512 through 530 removed outlier: 4.140A pdb=" N GLN A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 4.523A pdb=" N SER A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 573 No H-bonds generated for 'chain 'A' and resid 570 through 573' Processing helix chain 'A' and resid 578 through 592 removed outlier: 3.807A pdb=" N CYS A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 587 " --> pdb=" O GLN A 583 " (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 removed outlier: 3.757A pdb=" N LEU A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 673 through 683 removed outlier: 3.908A pdb=" N GLU A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 removed outlier: 3.556A pdb=" N ILE A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 722 through 735 removed outlier: 4.657A pdb=" N VAL A 726 " --> pdb=" O GLU A 723 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG A 727 " --> pdb=" O TYR A 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 239 removed outlier: 5.533A pdb=" N SER B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ARG B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 297 through 315 removed outlier: 4.103A pdb=" N ILE B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 333 No H-bonds generated for 'chain 'B' and resid 330 through 333' Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 376 through 378 No H-bonds generated for 'chain 'B' and resid 376 through 378' 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 416 removed outlier: 3.805A pdb=" N LEU B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG B 413 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 4.844A 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 438 through 455 removed outlier: 3.987A pdb=" N GLU B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 485 No H-bonds generated for 'chain 'B' and resid 482 through 485' Processing helix chain 'B' and resid 499 through 501 No H-bonds generated for 'chain 'B' and resid 499 through 501' Processing helix chain 'B' and resid 512 through 529 removed outlier: 3.533A pdb=" N LEU B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' Processing helix chain 'B' and resid 578 through 594 removed outlier: 3.707A pdb=" N ALA B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS B 594 " --> pdb=" O ASP B 590 " (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 631 removed outlier: 3.962A pdb=" N LYS B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 655 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 688 through 697 Processing helix chain 'B' and resid 707 through 718 removed outlier: 3.677A pdb=" N MET B 712 " --> pdb=" O LYS B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 734 removed outlier: 4.362A pdb=" N VAL B 726 " --> pdb=" O PRO B 722 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ARG B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 235 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 266 through 276 Processing helix chain 'C' and resid 297 through 308 removed outlier: 3.820A pdb=" N ILE C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASP C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 316 Processing helix chain 'C' and resid 348 through 358 removed outlier: 3.838A pdb=" N SER C 356 " --> pdb=" O ASN C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 378 No H-bonds generated for 'chain 'C' and resid 376 through 378' 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 400 through 416 removed outlier: 4.173A pdb=" N ARG C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N MET C 414 " --> pdb=" O HIS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 432 Processing helix chain 'C' and resid 439 through 456 removed outlier: 3.562A pdb=" N GLY C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 485 Processing helix chain 'C' and resid 512 through 530 Processing helix chain 'C' and resid 550 through 560 removed outlier: 3.760A pdb=" N ALA C 557 " --> pdb=" O ALA C 553 " (cutoff:3.500A) 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 630 Processing helix chain 'C' and resid 650 through 655 Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 688 through 698 removed outlier: 4.199A pdb=" N THR C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 694 " --> pdb=" O GLU C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 718 removed outlier: 3.787A pdb=" N MET C 712 " --> pdb=" O LYS C 708 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 737 removed outlier: 4.406A pdb=" N GLU C 735 " --> pdb=" O ALA C 731 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 234 Processing helix chain 'D' and resid 236 through 239 No H-bonds generated for 'chain 'D' and resid 236 through 239' Processing helix chain 'D' and resid 243 through 247 Processing helix chain 'D' and resid 266 through 275 removed outlier: 4.879A pdb=" N GLY D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 315 removed outlier: 3.619A pdb=" N ILE D 302 " --> pdb=" O SER D 298 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASP D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 358 removed outlier: 4.049A pdb=" N VAL D 351 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 355 " --> pdb=" O ASN D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 416 removed outlier: 3.937A pdb=" N HIS D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ARG D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 4.466A 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: 4.163A pdb=" N LEU D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG D 455 " --> pdb=" O THR D 451 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N HIS D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 488 Processing helix chain 'D' and resid 512 through 530 removed outlier: 4.131A pdb=" N GLN D 526 " --> pdb=" O GLU D 522 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR D 528 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 removed outlier: 3.695A pdb=" N ALA D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 593 removed outlier: 3.820A 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 621 through 631 removed outlier: 4.030A pdb=" N LYS D 631 " --> pdb=" O LEU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 637 No H-bonds generated for 'chain 'D' and resid 635 through 637' Processing helix chain 'D' and resid 652 through 655 No H-bonds generated for 'chain 'D' and resid 652 through 655' Processing helix chain 'D' and resid 657 through 660 No H-bonds generated for 'chain 'D' and resid 657 through 660' Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 688 through 695 Processing helix chain 'D' and resid 707 through 719 removed outlier: 4.313A pdb=" N MET D 712 " --> pdb=" O LYS D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 736 removed outlier: 4.399A pdb=" N VAL D 726 " --> pdb=" O PRO D 722 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 235 Processing helix chain 'E' and resid 266 through 277 Processing helix chain 'E' and resid 297 through 316 removed outlier: 4.561A pdb=" N ILE E 302 " --> pdb=" O SER E 298 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG E 303 " --> pdb=" O GLU E 299 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU E 305 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASP E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA E 309 " --> pdb=" O LEU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 333 No H-bonds generated for 'chain 'E' and resid 330 through 333' Processing helix chain 'E' and resid 352 through 359 Processing helix chain 'E' and resid 376 through 378 No H-bonds generated for 'chain 'E' and resid 376 through 378' Processing helix chain 'E' and resid 380 through 383 No H-bonds generated for 'chain 'E' and resid 380 through 383' Processing helix chain 'E' and resid 400 through 410 Processing helix chain 'E' and resid 412 through 415 No H-bonds generated for 'chain 'E' and resid 412 through 415' Processing helix chain 'E' and resid 426 through 432 removed outlier: 4.518A pdb=" N VAL E 431 " --> pdb=" O LYS E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 454 removed outlier: 3.765A pdb=" N THR E 451 " --> pdb=" O ALA E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 486 Processing helix chain 'E' and resid 512 through 530 Processing helix chain 'E' and resid 549 through 560 Processing helix chain 'E' and resid 578 through 583 Processing helix chain 'E' and resid 585 through 594 Processing helix chain 'E' and resid 605 through 609 Processing helix chain 'E' and resid 620 through 630 removed outlier: 4.635A pdb=" N LEU E 629 " --> pdb=" O ALA E 625 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU E 630 " --> pdb=" O LEU E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 654 Processing helix chain 'E' and resid 673 through 683 Processing helix chain 'E' and resid 688 through 697 removed outlier: 3.745A pdb=" N GLN E 696 " --> pdb=" O THR E 692 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN E 697 " --> pdb=" O THR E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 707 through 718 removed outlier: 3.638A pdb=" N GLU E 715 " --> pdb=" O LEU E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 735 removed outlier: 4.011A pdb=" N ALA E 731 " --> pdb=" O ARG E 727 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU E 735 " --> pdb=" O ALA E 731 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 502 No H-bonds generated for 'chain 'F' and resid 499 through 502' Processing helix chain 'F' and resid 512 through 529 removed outlier: 3.961A pdb=" N LEU F 524 " --> pdb=" O ASP F 520 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS F 529 " --> pdb=" O VAL F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 559 Processing helix chain 'F' and resid 578 through 594 removed outlier: 3.828A pdb=" N GLN F 583 " --> pdb=" O THR F 579 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP F 591 " --> pdb=" O LYS F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 608 No H-bonds generated for 'chain 'F' and resid 605 through 608' Processing helix chain 'F' and resid 620 through 630 Processing helix chain 'F' and resid 650 through 655 Processing helix chain 'F' and resid 673 through 683 Processing helix chain 'F' and resid 688 through 696 removed outlier: 3.920A pdb=" N THR F 693 " --> pdb=" O LYS F 689 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE F 694 " --> pdb=" O GLU F 690 " (cutoff:3.500A) Processing helix chain 'F' and resid 707 through 719 removed outlier: 4.078A pdb=" N GLU F 715 " --> pdb=" O LEU F 711 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N MET F 716 " --> pdb=" O MET F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 735 removed outlier: 3.556A pdb=" N LEU F 730 " --> pdb=" O VAL F 726 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA F 731 " --> pdb=" O ARG F 727 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 391 through 395 removed outlier: 4.072A pdb=" N VAL A 391 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ILE A 256 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL A 369 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU A 258 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLY A 371 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLY A 260 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N THR A 373 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N HIS A 323 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ILE A 370 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 325 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N MET A 372 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE A 327 " --> pdb=" O MET A 372 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 283 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 663 through 667 removed outlier: 3.741A pdb=" N THR A 663 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 540 " --> pdb=" O THR A 663 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 640 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N VAL A 539 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE A 642 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU A 541 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY A 644 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLY A 543 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 566 " --> pdb=" O CYS A 599 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 369 through 373 removed outlier: 5.898A pdb=" N VAL B 391 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR B 259 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N MET B 393 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 283 through 285 Processing sheet with id= E, first strand: chain 'B' and resid 663 through 666 removed outlier: 3.532A pdb=" N LEU B 540 " --> pdb=" O THR B 663 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N VAL B 539 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE B 642 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU B 541 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY B 644 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 566 " --> pdb=" O CYS B 599 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS B 568 " --> pdb=" O VAL B 601 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 391 through 395 removed outlier: 3.540A pdb=" N MET C 393 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY C 371 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N GLY C 260 " --> pdb=" O GLY C 371 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR C 373 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 323 through 326 removed outlier: 3.698A pdb=" N LEU C 368 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 663 through 667 removed outlier: 6.526A pdb=" N LEU C 640 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N VAL C 539 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE C 642 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU C 541 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY C 644 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N GLY C 543 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR C 646 " --> pdb=" O GLY C 543 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 392 through 394 removed outlier: 8.907A pdb=" N MET D 393 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 257 " --> pdb=" O MET D 393 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL D 369 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU D 258 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY D 371 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 663 through 667 removed outlier: 6.545A pdb=" N LEU D 640 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N VAL D 539 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE D 642 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU D 541 " --> pdb=" O ILE D 642 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY D 644 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLY D 543 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR D 646 " --> pdb=" O GLY D 543 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 283 through 285 Processing sheet with id= L, first strand: chain 'E' and resid 663 through 667 removed outlier: 6.538A pdb=" N ILE E 642 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N LEU E 541 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY E 644 " --> pdb=" O LEU E 541 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N GLY E 543 " --> pdb=" O GLY E 644 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR E 646 " --> pdb=" O GLY E 543 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP E 603 " --> pdb=" O CYS E 568 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 536 through 542 removed outlier: 6.580A pdb=" N LEU F 640 " --> pdb=" O VAL F 537 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL F 539 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE F 642 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU F 541 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLY F 644 " --> pdb=" O LEU F 541 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL F 600 " --> pdb=" O ILE F 643 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR F 645 " --> pdb=" O VAL F 600 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL F 602 " --> pdb=" O THR F 645 " (cutoff:3.500A) No H-bonds generated for sheet with id= M 730 hydrogen bonds defined for protein. 2091 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: 16.72 Time building geometry restraints manager: 35.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 22825 1.02 - 1.22: 45 1.22 - 1.42: 8880 1.42 - 1.62: 13756 1.62 - 1.82: 217 Bond restraints: 45723 Sorted by residual: bond pdb=" C4 ATP B 802 " pdb=" N9 ATP B 802 " ideal model delta sigma weight residual 1.374 1.300 0.074 1.00e-02 1.00e+04 5.41e+01 bond pdb=" C4 ATP F 801 " pdb=" C5 ATP F 801 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.10e+01 bond pdb=" C4 ATP E 801 " pdb=" C5 ATP E 801 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.01e+01 bond pdb=" C4 ATP D 801 " pdb=" C5 ATP D 801 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.86e+01 bond pdb=" C4 ATP C 802 " pdb=" C5 ATP C 802 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.60e+01 ... (remaining 45718 not shown) Histogram of bond angle deviations from ideal: 76.20 - 88.40: 31 88.40 - 100.60: 69 100.60 - 112.79: 55701 112.79 - 124.99: 25982 124.99 - 137.19: 1396 Bond angle restraints: 83179 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 113.53 26.34 1.00e+00 1.00e+00 6.94e+02 angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 114.01 25.86 1.00e+00 1.00e+00 6.69e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 111.28 25.55 1.00e+00 1.00e+00 6.53e+02 angle pdb=" PB ATP D 802 " pdb=" O3B ATP D 802 " pdb=" PG ATP D 802 " ideal model delta sigma weight residual 139.87 114.48 25.39 1.00e+00 1.00e+00 6.45e+02 angle pdb=" PB ATP B 802 " pdb=" O3B ATP B 802 " pdb=" PG ATP B 802 " ideal model delta sigma weight residual 139.87 114.85 25.02 1.00e+00 1.00e+00 6.26e+02 ... (remaining 83174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 20653 36.00 - 72.00: 561 72.00 - 107.99: 25 107.99 - 143.99: 5 143.99 - 179.99: 2 Dihedral angle restraints: 21246 sinusoidal: 12276 harmonic: 8970 Sorted by residual: dihedral pdb=" CA PRO D 613 " pdb=" C PRO D 613 " pdb=" N ILE D 614 " pdb=" CA ILE D 614 " ideal model delta harmonic sigma weight residual 180.00 101.34 78.66 0 5.00e+00 4.00e-02 2.47e+02 dihedral pdb=" CD ARG A 388 " pdb=" NE ARG A 388 " pdb=" CZ ARG A 388 " pdb=" NH1 ARG A 388 " ideal model delta sinusoidal sigma weight residual 0.00 179.99 -179.99 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA ASN C 214 " pdb=" C ASN C 214 " pdb=" N PHE C 215 " pdb=" CA PHE C 215 " ideal model delta harmonic sigma weight residual 180.00 134.43 45.57 0 5.00e+00 4.00e-02 8.31e+01 ... (remaining 21243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.561: 3522 0.561 - 1.122: 0 1.122 - 1.684: 0 1.684 - 2.245: 6 2.245 - 2.806: 1 Chirality restraints: 3529 Sorted by residual: chirality pdb=" CG LEU B 420 " pdb=" CB LEU B 420 " pdb=" CD1 LEU B 420 " pdb=" CD2 LEU B 420 " both_signs ideal model delta sigma weight residual False -2.59 0.22 -2.81 2.00e-01 2.50e+01 1.97e+02 chirality pdb=" CG LEU C 484 " pdb=" CB LEU C 484 " pdb=" CD1 LEU C 484 " pdb=" CD2 LEU C 484 " both_signs ideal model delta sigma weight residual False -2.59 -0.64 -1.95 2.00e-01 2.50e+01 9.49e+01 chirality pdb=" CG LEU E 713 " pdb=" CB LEU E 713 " pdb=" CD1 LEU E 713 " pdb=" CD2 LEU E 713 " both_signs ideal model delta sigma weight residual False -2.59 -0.65 -1.94 2.00e-01 2.50e+01 9.37e+01 ... (remaining 3526 not shown) Planarity restraints: 6639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 241 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C PRO D 241 " -0.059 2.00e-02 2.50e+03 pdb=" O PRO D 241 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO D 242 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 671 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C ALA B 671 " -0.058 2.00e-02 2.50e+03 pdb=" O ALA B 671 " 0.022 2.00e-02 2.50e+03 pdb=" N THR B 672 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 549 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C LYS F 549 " 0.057 2.00e-02 2.50e+03 pdb=" O LYS F 549 " -0.021 2.00e-02 2.50e+03 pdb=" N THR F 550 " -0.019 2.00e-02 2.50e+03 ... (remaining 6636 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 3958 2.21 - 2.81: 101029 2.81 - 3.40: 117445 3.40 - 4.00: 156150 4.00 - 4.60: 242020 Nonbonded interactions: 620602 Sorted by model distance: nonbonded pdb=" O LEU D 355 " pdb="HH12 ARG D 388 " model vdw 1.610 1.850 nonbonded pdb="HH21 ARG A 385 " pdb=" O1B ATP B 801 " model vdw 1.625 1.850 nonbonded pdb=" OE1 GLU A 390 " pdb="HH12 ARG B 446 " model vdw 1.627 1.850 nonbonded pdb=" H GLY B 222 " pdb=" OE1 GLN B 405 " model vdw 1.627 1.850 nonbonded pdb=" O GLU A 243 " pdb="HE22 GLN A 247 " model vdw 1.634 1.850 ... (remaining 620597 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 215 through 240 or resid 250 through 457 or resid 459 thro \ ugh 547 or (resid 548 and (name N or name CA or name C or name O or name HA2 or \ name HA3)) or resid 549 through 738 or resid 801)) selection = (chain 'B' and (resid 215 through 240 or resid 250 through 263 or (resid 264 and \ (name N or name CA or name C or name O or name CB or name SG or name HA or name \ HB2 or name HB3 or name HG )) or resid 265 through 387 or (resid 388 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 HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH1 \ 2 or name HH21)) or resid 389 through 457 or resid 459 or resid 477 through 547 \ or (resid 548 and (name N or name CA or name C or name O or name HA2 or name HA3 \ )) or resid 549 through 738 or resid 801)) selection = (chain 'C' and (resid 215 through 240 or resid 250 through 263 or (resid 264 and \ (name N or name CA or name C or name O or name CB or name SG or name HA or name \ HB2 or name HB3 or name HG )) or resid 265 through 387 or (resid 388 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 HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH1 \ 2 or name HH21)) or resid 389 through 457 or resid 470 or resid 477 through 547 \ or (resid 548 and (name N or name CA or name C or name O or name HA2 or name HA3 \ )) or resid 549 through 738 or resid 801)) selection = (chain 'D' and (resid 215 through 240 or resid 250 through 263 or (resid 264 and \ (name N or name CA or name C or name O or name CB or name SG or name HA or name \ HB2 or name HB3 or name HG )) or resid 265 through 387 or (resid 388 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 HB3 or \ name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name HH1 \ 2 or name HH21)) or resid 389 through 457 or resid 470 or resid 477 through 738 \ or resid 801)) selection = (chain 'E' and (resid 215 through 263 or (resid 264 and (name N or name CA or na \ me C or name O or name CB or name SG or name HA or name HB2 or name HB3 or name \ HG )) or resid 265 through 387 or (resid 388 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 na \ me NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21)) or resid \ 389 through 457 or resid 470 or resid 477 through 547 or (resid 548 and (name N \ or name CA or name C or name O or name HA2 or name HA3)) or resid 549 through 7 \ 38 or resid 801)) } 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: 0.830 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: 0.620 Extract box with map and model: 5.130 Check model and map are aligned: 0.630 Set scattering table: 0.370 Process input model: 134.610 Find NCS groups from input model: 2.270 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 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 : 0.015 0.138 22865 Z= 0.964 Angle : 1.436 26.338 30876 Z= 0.933 Chirality : 0.115 2.806 3529 Planarity : 0.007 0.067 3934 Dihedral : 14.298 179.987 9033 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.65 % Rotamer: Outliers : 0.16 % Allowed : 7.33 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.59 % 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: -3.28 (0.13), residues: 2817 helix: -2.41 (0.12), residues: 1276 sheet: -1.69 (0.22), residues: 337 loop : -1.85 (0.14), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP B 213 HIS 0.016 0.003 HIS C 347 PHE 0.028 0.004 PHE D 240 TYR 0.036 0.004 TYR F 593 ARG 0.021 0.002 ARG C 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 227 time to evaluate : 3.479 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 231 average time/residue: 0.9020 time to fit residues: 314.3466 Evaluate side-chains 162 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 477 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 237 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 255 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN B 365 ASN B 454 ASN B 505 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN C 272 GLN C 374 ASN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN C 696 GLN D 418 GLN ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 697 GLN E 352 ASN E 435 ASN ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 ASN E 675 GLN ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 675 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22865 Z= 0.215 Angle : 0.681 12.205 30876 Z= 0.355 Chirality : 0.079 1.795 3529 Planarity : 0.004 0.044 3934 Dihedral : 12.749 178.484 3355 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.28 % Allowed : 10.47 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.22 (0.14), residues: 2817 helix: -1.33 (0.13), residues: 1269 sheet: -1.07 (0.24), residues: 307 loop : -1.58 (0.16), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 510 HIS 0.006 0.001 HIS C 410 PHE 0.017 0.002 PHE F 661 TYR 0.013 0.002 TYR B 593 ARG 0.006 0.001 ARG E 415 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 4.025 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.2799 (ttm) cc_final: 0.2183 (ttp) REVERT: D 655 MET cc_start: 0.6572 (mtp) cc_final: 0.5998 (mtm) REVERT: E 716 MET cc_start: 0.6856 (mtp) cc_final: 0.6608 (mtp) outliers start: 31 outliers final: 19 residues processed: 192 average time/residue: 0.8598 time to fit residues: 252.3563 Evaluate side-chains 179 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 669 ASN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 724 TYR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 504 MET Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain E residue 724 TYR Chi-restraints excluded: chain F residue 588 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 141 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 255 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 253 optimal weight: 0.4980 chunk 87 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22865 Z= 0.266 Angle : 0.644 10.880 30876 Z= 0.340 Chirality : 0.079 1.807 3529 Planarity : 0.004 0.039 3934 Dihedral : 11.925 178.661 3355 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.99 % Allowed : 11.99 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.86 (0.14), residues: 2817 helix: -0.92 (0.13), residues: 1263 sheet: -0.86 (0.25), residues: 328 loop : -1.55 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 213 HIS 0.005 0.001 HIS C 410 PHE 0.011 0.001 PHE D 227 TYR 0.013 0.002 TYR D 502 ARG 0.004 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 3.621 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 172 average time/residue: 0.8955 time to fit residues: 232.3412 Evaluate side-chains 167 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 3.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 724 TYR Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 504 MET Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain E residue 657 MET Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 588 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 252 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 256 optimal weight: 0.6980 chunk 271 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 243 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22865 Z= 0.214 Angle : 0.610 11.395 30876 Z= 0.316 Chirality : 0.079 1.785 3529 Planarity : 0.004 0.038 3934 Dihedral : 11.317 178.309 3355 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.03 % Allowed : 12.86 % 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: -1.61 (0.14), residues: 2817 helix: -0.64 (0.14), residues: 1268 sheet: -0.79 (0.25), residues: 337 loop : -1.51 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 213 HIS 0.005 0.001 HIS C 410 PHE 0.013 0.001 PHE B 589 TYR 0.011 0.001 TYR D 502 ARG 0.005 0.000 ARG D 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 3.992 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: B 248 MET cc_start: 0.6567 (ptt) cc_final: 0.6255 (ptt) outliers start: 25 outliers final: 17 residues processed: 172 average time/residue: 0.8865 time to fit residues: 235.0081 Evaluate side-chains 162 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 3.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 724 TYR Chi-restraints excluded: chain C residue 504 MET Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 626 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 226 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 202 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 231 optimal weight: 0.0670 chunk 187 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 overall best weight: 2.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22865 Z= 0.204 Angle : 0.596 11.362 30876 Z= 0.306 Chirality : 0.078 1.763 3529 Planarity : 0.004 0.078 3934 Dihedral : 10.849 178.503 3355 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.15 % Allowed : 13.23 % Favored : 85.62 % 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: -1.36 (0.15), residues: 2817 helix: -0.32 (0.14), residues: 1270 sheet: -0.84 (0.25), residues: 350 loop : -1.45 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 213 HIS 0.004 0.001 HIS C 410 PHE 0.011 0.001 PHE D 227 TYR 0.009 0.001 TYR D 502 ARG 0.018 0.000 ARG F 734 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 3.603 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: B 657 MET cc_start: 0.7388 (ppp) cc_final: 0.7039 (ppp) REVERT: D 319 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8118 (p0) outliers start: 28 outliers final: 21 residues processed: 168 average time/residue: 0.8474 time to fit residues: 221.0515 Evaluate side-chains 169 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 3.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 724 TYR Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 504 MET Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 655 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 91 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 22865 Z= 0.303 Angle : 0.636 11.289 30876 Z= 0.335 Chirality : 0.078 1.775 3529 Planarity : 0.004 0.036 3934 Dihedral : 10.936 179.196 3355 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.36 % Allowed : 14.01 % Favored : 84.63 % 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: -1.57 (0.14), residues: 2817 helix: -0.50 (0.13), residues: 1273 sheet: -0.93 (0.25), residues: 352 loop : -1.57 (0.16), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 213 HIS 0.005 0.001 HIS B 456 PHE 0.013 0.001 PHE E 729 TYR 0.014 0.002 TYR C 724 ARG 0.010 0.001 ARG F 734 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 3.302 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: D 319 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8361 (p0) REVERT: F 657 MET cc_start: 0.8021 (ppp) cc_final: 0.7305 (ppp) outliers start: 33 outliers final: 24 residues processed: 165 average time/residue: 0.8783 time to fit residues: 222.5141 Evaluate side-chains 167 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 3.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 504 MET Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 655 MET Chi-restraints excluded: chain H residue 7 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 262 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 198 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 GLN ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22865 Z= 0.167 Angle : 0.585 11.299 30876 Z= 0.295 Chirality : 0.078 1.747 3529 Planarity : 0.003 0.034 3934 Dihedral : 10.640 179.514 3355 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.07 % Allowed : 14.59 % Favored : 84.34 % 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: -1.21 (0.15), residues: 2817 helix: -0.11 (0.14), residues: 1275 sheet: -0.89 (0.25), residues: 353 loop : -1.46 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 213 HIS 0.004 0.001 HIS E 323 PHE 0.013 0.001 PHE D 227 TYR 0.008 0.001 TYR E 611 ARG 0.005 0.000 ARG F 734 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 3.832 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: D 319 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8228 (p0) REVERT: D 712 MET cc_start: 0.6360 (mmm) cc_final: 0.6042 (tpp) outliers start: 26 outliers final: 21 residues processed: 165 average time/residue: 0.8723 time to fit residues: 218.0278 Evaluate side-chains 170 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 3.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 504 MET Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 319 ASN Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 502 TYR Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 655 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 167 optimal weight: 40.0000 chunk 108 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22865 Z= 0.322 Angle : 0.648 11.148 30876 Z= 0.343 Chirality : 0.078 1.767 3529 Planarity : 0.004 0.037 3934 Dihedral : 10.805 179.856 3355 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 1.32 % Allowed : 14.38 % Favored : 84.30 % 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: -1.55 (0.15), residues: 2817 helix: -0.42 (0.14), residues: 1265 sheet: -1.00 (0.25), residues: 352 loop : -1.61 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 213 HIS 0.006 0.001 HIS B 456 PHE 0.019 0.002 PHE B 215 TYR 0.016 0.002 TYR C 724 ARG 0.006 0.001 ARG F 734 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 3.505 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: D 712 MET cc_start: 0.6496 (mmm) cc_final: 0.6171 (tpp) outliers start: 32 outliers final: 25 residues processed: 162 average time/residue: 0.8443 time to fit residues: 209.6540 Evaluate side-chains 167 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 504 MET Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain H residue 7 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 246 optimal weight: 8.9990 chunk 259 optimal weight: 0.6980 chunk 236 optimal weight: 5.9990 chunk 252 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 251 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 ASN E 696 GLN ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 561 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22865 Z= 0.162 Angle : 0.590 11.338 30876 Z= 0.295 Chirality : 0.079 1.750 3529 Planarity : 0.004 0.032 3934 Dihedral : 10.526 178.953 3355 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.95 % Allowed : 14.71 % Favored : 84.34 % 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: -1.11 (0.15), residues: 2817 helix: 0.02 (0.14), residues: 1275 sheet: -0.86 (0.25), residues: 354 loop : -1.46 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 213 HIS 0.004 0.001 HIS E 323 PHE 0.027 0.001 PHE A 436 TYR 0.007 0.001 TYR C 724 ARG 0.005 0.000 ARG F 734 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 3.596 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: D 712 MET cc_start: 0.6480 (mmm) cc_final: 0.6082 (tpp) outliers start: 23 outliers final: 20 residues processed: 158 average time/residue: 0.8796 time to fit residues: 212.2454 Evaluate side-chains 167 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 4.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 504 MET Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 655 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 165 optimal weight: 0.7980 chunk 266 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 chunk 222 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22865 Z= 0.197 Angle : 0.596 11.164 30876 Z= 0.302 Chirality : 0.078 1.735 3529 Planarity : 0.004 0.037 3934 Dihedral : 10.375 179.485 3355 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.78 % Allowed : 15.12 % Favored : 84.10 % 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: -1.05 (0.15), residues: 2817 helix: 0.08 (0.14), residues: 1270 sheet: -0.78 (0.26), residues: 355 loop : -1.45 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 213 HIS 0.004 0.001 HIS E 323 PHE 0.023 0.001 PHE A 436 TYR 0.009 0.001 TYR C 724 ARG 0.012 0.001 ARG B 607 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5634 Ramachandran restraints generated. 2817 Oldfield, 0 Emsley, 2817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 14 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 3.560 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: D 712 MET cc_start: 0.6439 (mmm) cc_final: 0.6088 (tpp) outliers start: 19 outliers final: 18 residues processed: 155 average time/residue: 0.8096 time to fit residues: 194.0957 Evaluate side-chains 164 residues out of total 2427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 3.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 504 MET Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 504 MET Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 ARG Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain E residue 655 MET Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 655 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 177 optimal weight: 9.9990 chunk 237 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 205 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 229 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 505 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 = 0.2776 r_free = 0.2776 target = 0.031441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.024790 restraints weight = 597498.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.026139 restraints weight = 298295.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.027083 restraints weight = 182988.024| |-----------------------------------------------------------------------------| r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22865 Z= 0.236 Angle : 0.612 11.146 30876 Z= 0.314 Chirality : 0.078 1.743 3529 Planarity : 0.004 0.045 3934 Dihedral : 10.370 179.822 3355 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.87 % Allowed : 14.96 % Favored : 84.18 % 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: -1.22 (0.15), residues: 2817 helix: -0.07 (0.14), residues: 1270 sheet: -0.82 (0.26), residues: 357 loop : -1.55 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 213 HIS 0.005 0.001 HIS B 456 PHE 0.022 0.001 PHE A 436 TYR 0.012 0.001 TYR C 724 ARG 0.007 0.001 ARG B 607 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6637.04 seconds wall clock time: 119 minutes 50.93 seconds (7190.93 seconds total)