Starting phenix.real_space_refine on Mon Mar 18 11:48:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7klu_22918/03_2024/7klu_22918_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7klu_22918/03_2024/7klu_22918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7klu_22918/03_2024/7klu_22918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7klu_22918/03_2024/7klu_22918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7klu_22918/03_2024/7klu_22918_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7klu_22918/03_2024/7klu_22918_updated.pdb" } resolution = 3.5 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 Anisotropic ADP refinement not supported. Converting 1044 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 12 5.49 5 Mg 4 5.21 5 S 88 5.16 5 C 12466 2.51 5 N 3430 2.21 5 O 3738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 541": "OE1" <-> "OE2" Residue "A PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 658": "NH1" <-> "NH2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 185": "OD1" <-> "OD2" Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B ASP 416": "OD1" <-> "OD2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "B GLU 529": "OE1" <-> "OE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B ASP 604": "OD1" <-> "OD2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ARG 658": "NH1" <-> "NH2" Residue "B TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 334": "OD1" <-> "OD2" Residue "D TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 347": "OD1" <-> "OD2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ASP 392": "OD1" <-> "OD2" Residue "D GLU 394": "OE1" <-> "OE2" Residue "D ARG 402": "NH1" <-> "NH2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 449": "NH1" <-> "NH2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D ASP 463": "OD1" <-> "OD2" Residue "D GLU 523": "OE1" <-> "OE2" Residue "D PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 533": "OE1" <-> "OE2" Residue "D PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 643": "OE1" <-> "OE2" Residue "D ARG 658": "NH1" <-> "NH2" Residue "D GLU 695": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 263": "OE1" <-> "OE2" Residue "C ASP 272": "OD1" <-> "OD2" Residue "C ARG 291": "NH1" <-> "NH2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C GLU 403": "OE1" <-> "OE2" Residue "C ASP 416": "OD1" <-> "OD2" Residue "C GLU 442": "OE1" <-> "OE2" Residue "C TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 449": "NH1" <-> "NH2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 523": "OE1" <-> "OE2" Residue "C GLU 529": "OE1" <-> "OE2" Residue "C PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 541": "OE1" <-> "OE2" Residue "C GLU 581": "OE1" <-> "OE2" Residue "C GLU 632": "OE1" <-> "OE2" Residue "C GLU 633": "OE1" <-> "OE2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C ARG 658": "NH1" <-> "NH2" Residue "C ASP 670": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19742 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4890 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 18, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4915 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 18, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4890 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 18, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 4915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4915 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 18, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.34, per 1000 atoms: 0.52 Number of scatterers: 19742 At special positions: 0 Unit cell: (168.062, 131.564, 134.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 88 16.00 P 12 15.00 Mg 4 11.99 O 3738 8.00 N 3430 7.00 C 12466 6.00 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: 6.94 Conformation dependent library (CDL) restraints added in 3.5 seconds 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4676 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 16 sheets defined 39.8% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.92 Creating SS restraints... Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 112 through 134 Processing helix chain 'A' and resid 165 through 172 Processing helix chain 'A' and resid 179 through 186 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 262 through 265 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.681A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 432 removed outlier: 3.538A pdb=" N LYS A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 454 removed outlier: 3.562A pdb=" N LYS A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 467 removed outlier: 3.530A pdb=" N LYS A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 489 removed outlier: 3.793A pdb=" N ALA A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 510 Processing helix chain 'A' and resid 512 through 518 removed outlier: 3.514A pdb=" N ALA A 516 " --> pdb=" O PRO A 512 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 517 " --> pdb=" O TYR A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 550 through 555 removed outlier: 3.984A pdb=" N VAL A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 587 removed outlier: 4.419A pdb=" N GLU A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 592 No H-bonds generated for 'chain 'A' and resid 590 through 592' Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.934A pdb=" N ARG A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 658 removed outlier: 4.165A pdb=" N ASN A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 680 removed outlier: 3.676A pdb=" N LEU A 667 " --> pdb=" O GLY A 663 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 700 removed outlier: 3.592A pdb=" N MET A 689 " --> pdb=" O PRO A 686 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 690 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY A 691 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 692 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN A 694 " --> pdb=" O GLY A 691 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU A 695 " --> pdb=" O ARG A 692 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 698 " --> pdb=" O GLU A 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 111 through 133 Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 179 through 187 Processing helix chain 'B' and resid 205 through 210 removed outlier: 3.705A pdb=" N PHE B 209 " --> pdb=" O TYR B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 352 through 355 No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 409 through 432 removed outlier: 3.552A pdb=" N LYS B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 416 " --> pdb=" O ARG B 412 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS B 431 " --> pdb=" O ILE B 427 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 443 Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.697A pdb=" N VAL B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 467 removed outlier: 3.563A pdb=" N GLU B 462 " --> pdb=" O GLN B 458 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 463 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 487 Processing helix chain 'B' and resid 505 through 509 Processing helix chain 'B' and resid 512 through 519 removed outlier: 4.860A pdb=" N LYS B 519 " --> pdb=" O GLU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 removed outlier: 3.655A pdb=" N LEU B 537 " --> pdb=" O GLU B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 556 removed outlier: 3.511A pdb=" N ILE B 554 " --> pdb=" O VAL B 550 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 589 removed outlier: 3.785A pdb=" N MET B 586 " --> pdb=" O LEU B 582 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 624 removed outlier: 3.655A pdb=" N HIS B 620 " --> pdb=" O GLY B 616 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET B 624 " --> pdb=" O HIS B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 Processing helix chain 'B' and resid 649 through 660 removed outlier: 3.846A pdb=" N ASN B 655 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER B 660 " --> pdb=" O GLN B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 680 removed outlier: 3.840A pdb=" N LEU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP B 670 " --> pdb=" O GLN B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 700 removed outlier: 3.538A pdb=" N VAL B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 removed outlier: 3.757A pdb=" N ASP D 99 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 134 removed outlier: 3.644A pdb=" N ILE D 113 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS D 129 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL D 132 " --> pdb=" O HIS D 129 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 133 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 171 removed outlier: 3.510A pdb=" N VAL D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 185 Processing helix chain 'D' and resid 205 through 210 Processing helix chain 'D' and resid 259 through 265 removed outlier: 4.029A pdb=" N LYS D 262 " --> pdb=" O SER D 259 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLU D 263 " --> pdb=" O ASP D 260 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE D 264 " --> pdb=" O CYS D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 277 Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 308 through 318 removed outlier: 3.885A pdb=" N TYR D 315 " --> pdb=" O HIS D 311 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR D 317 " --> pdb=" O GLU D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 432 Processing helix chain 'D' and resid 434 through 443 removed outlier: 3.501A pdb=" N ASP D 443 " --> pdb=" O LYS D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 453 Processing helix chain 'D' and resid 458 through 467 removed outlier: 4.485A pdb=" N LEU D 467 " --> pdb=" O ASP D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 488 Processing helix chain 'D' and resid 505 through 509 Processing helix chain 'D' and resid 512 through 519 removed outlier: 4.669A pdb=" N LYS D 519 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 550 through 556 removed outlier: 3.873A pdb=" N VAL D 555 " --> pdb=" O GLU D 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 556 " --> pdb=" O THR D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 590 removed outlier: 3.579A pdb=" N TRP D 585 " --> pdb=" O GLU D 581 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET D 586 " --> pdb=" O LEU D 582 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG D 587 " --> pdb=" O MET D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 627 removed outlier: 4.183A pdb=" N ARG D 623 " --> pdb=" O ARG D 619 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN D 626 " --> pdb=" O LEU D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 656 removed outlier: 3.856A pdb=" N ASN D 655 " --> pdb=" O ILE D 651 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN D 656 " --> pdb=" O LYS D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 679 removed outlier: 3.804A pdb=" N LEU D 667 " --> pdb=" O GLY D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 700 removed outlier: 4.287A pdb=" N ARG D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS D 699 " --> pdb=" O GLU D 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 103 removed outlier: 4.043A pdb=" N LEU C 98 " --> pdb=" O THR C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 removed outlier: 3.761A pdb=" N PHE C 112 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE C 113 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 114 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU C 115 " --> pdb=" O PHE C 112 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 117 " --> pdb=" O ARG C 114 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU C 124 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 170 removed outlier: 3.710A pdb=" N VAL C 169 " --> pdb=" O GLN C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 185 Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 262 through 265 removed outlier: 3.517A pdb=" N SER C 265 " --> pdb=" O LYS C 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 267 through 278 removed outlier: 3.577A pdb=" N VAL C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 308 through 318 Processing helix chain 'C' and resid 352 through 355 No H-bonds generated for 'chain 'C' and resid 352 through 355' Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 409 through 432 removed outlier: 4.119A pdb=" N ARG C 415 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP C 416 " --> pdb=" O ARG C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 458 through 467 removed outlier: 3.550A pdb=" N LYS C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU C 467 " --> pdb=" O ASP C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 505 through 509 Processing helix chain 'C' and resid 512 through 519 removed outlier: 5.057A pdb=" N LYS C 519 " --> pdb=" O GLU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 550 through 556 Processing helix chain 'C' and resid 576 through 589 removed outlier: 3.935A pdb=" N LEU C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA C 584 " --> pdb=" O GLU C 580 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TRP C 585 " --> pdb=" O GLU C 581 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET C 586 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG C 587 " --> pdb=" O MET C 583 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN C 588 " --> pdb=" O ALA C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 624 removed outlier: 4.300A pdb=" N ARG C 623 " --> pdb=" O ARG C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 636 Processing helix chain 'C' and resid 649 through 656 removed outlier: 3.554A pdb=" N ASN C 655 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN C 656 " --> pdb=" O LYS C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 679 removed outlier: 3.992A pdb=" N GLN C 666 " --> pdb=" O PRO C 662 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU C 667 " --> pdb=" O GLY C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 700 removed outlier: 3.873A pdb=" N GLY C 691 " --> pdb=" O ALA C 688 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN C 694 " --> pdb=" O GLY C 691 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL C 698 " --> pdb=" O GLU C 695 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C 700 " --> pdb=" O LEU C 697 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 285 through 287 removed outlier: 6.718A pdb=" N ILE A 143 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 251 " --> pdb=" O ASP A 158 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 233 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER A 219 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 228 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 388 through 390 removed outlier: 3.746A pdb=" N TYR A 327 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 547 through 549 removed outlier: 5.687A pdb=" N ILE A 497 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 608 through 611 removed outlier: 7.847A pdb=" N LEU A 642 " --> pdb=" O THR A 595 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL A 597 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE A 644 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL A 599 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 285 through 287 removed outlier: 6.361A pdb=" N ILE B 143 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG B 214 " --> pdb=" O HIS B 256 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER B 219 " --> pdb=" O TYR B 229 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 327 through 333 removed outlier: 3.824A pdb=" N TYR B 327 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 345 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 364 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 546 through 549 removed outlier: 4.116A pdb=" N TYR B 499 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 597 through 599 removed outlier: 6.654A pdb=" N LEU B 642 " --> pdb=" O LYS B 598 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR B 641 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 284 through 287 removed outlier: 4.199A pdb=" N ARG D 214 " --> pdb=" O HIS D 256 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 233 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 228 " --> pdb=" O ALA D 244 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 327 through 333 removed outlier: 3.801A pdb=" N TYR D 327 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 345 " --> pdb=" O TYR D 327 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 498 through 501 Processing sheet with id= L, first strand: chain 'D' and resid 597 through 599 removed outlier: 6.242A pdb=" N LEU D 642 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 284 through 287 removed outlier: 3.709A pdb=" N THR C 251 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY C 250 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG C 214 " --> pdb=" O HIS C 256 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER C 219 " --> pdb=" O TYR C 229 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 242 " --> pdb=" O GLN C 230 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 327 through 333 removed outlier: 3.813A pdb=" N TYR C 327 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 364 " --> pdb=" O GLY C 389 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 546 through 549 Processing sheet with id= P, first strand: chain 'C' and resid 596 through 599 685 hydrogen bonds defined for protein. 1845 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: 6.27 Time building geometry restraints manager: 7.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6517 1.34 - 1.46: 4029 1.46 - 1.58: 9360 1.58 - 1.70: 20 1.70 - 1.81: 160 Bond restraints: 20086 Sorted by residual: bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.15e+01 bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" O3A ANP C 901 " pdb=" PB ANP C 901 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" O3A ANP D 901 " pdb=" PB ANP D 901 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" N3B ANP C 901 " pdb=" PG ANP C 901 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.68e+01 ... (remaining 20081 not shown) Histogram of bond angle deviations from ideal: 99.25 - 106.23: 450 106.23 - 113.21: 11015 113.21 - 120.19: 7193 120.19 - 127.17: 8263 127.17 - 134.15: 185 Bond angle restraints: 27106 Sorted by residual: angle pdb=" PB ANP B 901 " pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 126.95 110.16 16.79 3.00e+00 1.11e-01 3.13e+01 angle pdb=" PB ANP A 901 " pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 126.95 110.30 16.65 3.00e+00 1.11e-01 3.08e+01 angle pdb=" PB ANP D 901 " pdb=" N3B ANP D 901 " pdb=" PG ANP D 901 " ideal model delta sigma weight residual 126.95 110.33 16.62 3.00e+00 1.11e-01 3.07e+01 angle pdb=" PB ANP C 901 " pdb=" N3B ANP C 901 " pdb=" PG ANP C 901 " ideal model delta sigma weight residual 126.95 110.41 16.54 3.00e+00 1.11e-01 3.04e+01 angle pdb=" O1B ANP C 901 " pdb=" PB ANP C 901 " pdb=" O2B ANP C 901 " ideal model delta sigma weight residual 120.08 109.09 10.99 3.00e+00 1.11e-01 1.34e+01 ... (remaining 27101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 10977 17.92 - 35.85: 1091 35.85 - 53.77: 189 53.77 - 71.70: 59 71.70 - 89.62: 46 Dihedral angle restraints: 12362 sinusoidal: 5166 harmonic: 7196 Sorted by residual: dihedral pdb=" CA ASP A 158 " pdb=" CB ASP A 158 " pdb=" CG ASP A 158 " pdb=" OD1 ASP A 158 " ideal model delta sinusoidal sigma weight residual -30.00 -86.73 56.73 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CB GLU A 462 " pdb=" CG GLU A 462 " pdb=" CD GLU A 462 " pdb=" OE1 GLU A 462 " ideal model delta sinusoidal sigma weight residual 0.00 89.62 -89.62 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 216 " pdb=" CG GLU A 216 " pdb=" CD GLU A 216 " pdb=" OE1 GLU A 216 " ideal model delta sinusoidal sigma weight residual 0.00 89.52 -89.52 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 12359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2630 0.056 - 0.111: 395 0.111 - 0.167: 27 0.167 - 0.223: 0 0.223 - 0.278: 4 Chirality restraints: 3056 Sorted by residual: chirality pdb=" C3' ANP C 901 " pdb=" C2' ANP C 901 " pdb=" C4' ANP C 901 " pdb=" O3' ANP C 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3' ANP D 901 " pdb=" C2' ANP D 901 " pdb=" C4' ANP D 901 " pdb=" O3' ANP D 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 3053 not shown) Planarity restraints: 3440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 223 " -0.050 5.00e-02 4.00e+02 7.62e-02 9.30e+00 pdb=" N PRO D 224 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 224 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 224 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 302 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO B 303 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 303 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 303 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 138 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO D 139 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 139 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 139 " 0.019 5.00e-02 4.00e+02 ... (remaining 3437 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.63: 215 2.63 - 3.26: 19781 3.26 - 3.89: 36571 3.89 - 4.51: 48960 4.51 - 5.14: 77653 Nonbonded interactions: 183180 Sorted by model distance: nonbonded pdb=" O3G ANP B 901 " pdb="MG MG B 902 " model vdw 2.005 2.170 nonbonded pdb=" OD1 ASN B 119 " pdb="MG MG B 902 " model vdw 2.014 2.170 nonbonded pdb=" OD1 ASN D 119 " pdb="MG MG D 902 " model vdw 2.054 2.170 nonbonded pdb=" O3G ANP A 901 " pdb="MG MG A 902 " model vdw 2.059 2.170 nonbonded pdb=" O3G ANP D 901 " pdb="MG MG D 902 " model vdw 2.063 2.170 ... (remaining 183175 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 70 through 355 or resid 361 through 626 or resid 631 throu \ gh 704 or resid 901 through 903)) selection = (chain 'B' and (resid 70 through 355 or resid 361 through 625 or resid 631 or re \ sid 636 through 704 or resid 901 through 903)) selection = (chain 'C' and (resid 70 through 355 or resid 361 through 625 or resid 631 or re \ sid 636 through 704 or resid 901 through 903)) selection = (chain 'D' and (resid 70 through 355 or resid 361 through 626 or resid 631 throu \ gh 704 or resid 901 through 903)) } 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 8.230 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 52.780 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 : 0.004 0.144 20086 Z= 0.223 Angle : 0.602 16.792 27106 Z= 0.291 Chirality : 0.040 0.278 3056 Planarity : 0.003 0.076 3440 Dihedral : 15.723 89.620 7686 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2420 helix: 0.11 (0.17), residues: 972 sheet: 0.33 (0.29), residues: 358 loop : -1.27 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 585 HIS 0.004 0.000 HIS B 129 PHE 0.020 0.001 PHE A 183 TYR 0.019 0.001 TYR B 673 ARG 0.005 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 ASN cc_start: 0.8123 (m-40) cc_final: 0.7847 (m110) REVERT: A 623 ARG cc_start: 0.6037 (ttp-170) cc_final: 0.5691 (tpt170) REVERT: B 308 GLU cc_start: 0.6335 (tp30) cc_final: 0.6119 (tp30) REVERT: B 352 MET cc_start: 0.2527 (mmm) cc_final: 0.1927 (ptp) REVERT: C 689 MET cc_start: 0.7825 (ppp) cc_final: 0.6753 (ppp) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.3155 time to fit residues: 85.9833 Evaluate side-chains 143 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 10.0000 chunk 184 optimal weight: 0.0040 chunk 102 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 221 optimal weight: 4.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 171 ASN A 288 ASN A 310 GLN A 496 ASN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 530 GLN ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20086 Z= 0.271 Angle : 0.560 8.820 27106 Z= 0.290 Chirality : 0.042 0.167 3056 Planarity : 0.004 0.055 3440 Dihedral : 6.652 59.588 2804 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.84 % Allowed : 7.47 % Favored : 91.69 % 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: -1.00 (0.17), residues: 2420 helix: -0.04 (0.17), residues: 1010 sheet: 0.25 (0.27), residues: 380 loop : -1.61 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 585 HIS 0.008 0.001 HIS A 620 PHE 0.021 0.002 PHE D 621 TYR 0.019 0.001 TYR C 317 ARG 0.005 0.000 ARG C 388 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 309 TRP cc_start: 0.5921 (t60) cc_final: 0.5678 (t-100) REVERT: B 352 MET cc_start: 0.2935 (mmm) cc_final: 0.2126 (ptp) REVERT: B 479 GLN cc_start: 0.6879 (mp10) cc_final: 0.6519 (mp10) REVERT: D 240 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7359 (tm-30) REVERT: D 622 LEU cc_start: 0.7424 (mm) cc_final: 0.7047 (mm) REVERT: C 292 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8078 (ptp) REVERT: C 624 MET cc_start: 0.4200 (mtt) cc_final: 0.3969 (mtm) outliers start: 18 outliers final: 13 residues processed: 152 average time/residue: 0.3019 time to fit residues: 72.6020 Evaluate side-chains 147 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 596 ASN Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 496 ASN Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 609 MET Chi-restraints excluded: chain C residue 672 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 221 optimal weight: 1.9990 chunk 239 optimal weight: 10.0000 chunk 197 optimal weight: 0.0570 chunk 220 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 0.0970 overall best weight: 2.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20086 Z= 0.202 Angle : 0.494 6.850 27106 Z= 0.257 Chirality : 0.040 0.153 3056 Planarity : 0.003 0.039 3440 Dihedral : 6.144 59.084 2804 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.93 % Allowed : 11.30 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.17), residues: 2420 helix: 0.06 (0.17), residues: 998 sheet: 0.29 (0.27), residues: 380 loop : -1.63 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 585 HIS 0.004 0.001 HIS B 129 PHE 0.017 0.001 PHE A 183 TYR 0.010 0.001 TYR C 317 ARG 0.006 0.000 ARG C 388 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 309 TRP cc_start: 0.5837 (t60) cc_final: 0.5538 (t-100) REVERT: B 352 MET cc_start: 0.3052 (mmm) cc_final: 0.2172 (ptp) REVERT: D 622 LEU cc_start: 0.7429 (mm) cc_final: 0.7038 (mm) REVERT: C 292 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8110 (ptp) outliers start: 20 outliers final: 10 residues processed: 150 average time/residue: 0.3051 time to fit residues: 72.1580 Evaluate side-chains 142 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 609 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 115 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 222 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 211 optimal weight: 0.0170 chunk 63 optimal weight: 7.9990 overall best weight: 2.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20086 Z= 0.252 Angle : 0.514 7.460 27106 Z= 0.266 Chirality : 0.041 0.182 3056 Planarity : 0.003 0.033 3440 Dihedral : 6.028 56.144 2804 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.26 % Allowed : 13.31 % Favored : 85.43 % 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: -1.03 (0.17), residues: 2420 helix: 0.01 (0.17), residues: 998 sheet: 0.24 (0.27), residues: 380 loop : -1.70 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 231 HIS 0.005 0.001 HIS A 620 PHE 0.018 0.001 PHE A 183 TYR 0.011 0.001 TYR B 673 ARG 0.005 0.000 ARG C 388 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 2.761 Fit side-chains revert: symmetry clash REVERT: A 651 ILE cc_start: 0.8238 (mm) cc_final: 0.7783 (mm) REVERT: B 309 TRP cc_start: 0.5941 (t60) cc_final: 0.5652 (t-100) REVERT: B 352 MET cc_start: 0.3237 (mmm) cc_final: 0.2246 (ptp) REVERT: D 622 LEU cc_start: 0.7480 (mm) cc_final: 0.7089 (mm) REVERT: C 292 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7885 (ptp) outliers start: 27 outliers final: 17 residues processed: 161 average time/residue: 0.3014 time to fit residues: 77.8972 Evaluate side-chains 152 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 596 ASN Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 609 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 59 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 148 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 20086 Z= 0.411 Angle : 0.626 7.552 27106 Z= 0.325 Chirality : 0.045 0.162 3056 Planarity : 0.004 0.051 3440 Dihedral : 6.561 57.761 2804 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.59 % Allowed : 15.97 % Favored : 82.45 % 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: -1.39 (0.17), residues: 2420 helix: -0.25 (0.17), residues: 976 sheet: -0.06 (0.26), residues: 394 loop : -1.90 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 231 HIS 0.007 0.001 HIS A 311 PHE 0.019 0.002 PHE A 183 TYR 0.013 0.002 TYR B 673 ARG 0.006 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 490 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6805 (ptm) REVERT: B 187 LEU cc_start: 0.5924 (tp) cc_final: 0.5573 (tp) REVERT: D 551 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: D 622 LEU cc_start: 0.7545 (mm) cc_final: 0.7164 (mm) outliers start: 34 outliers final: 22 residues processed: 159 average time/residue: 0.2801 time to fit residues: 72.5642 Evaluate side-chains 155 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 551 GLU Chi-restraints excluded: chain D residue 596 ASN Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 2.9990 chunk 212 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20086 Z= 0.293 Angle : 0.551 8.486 27106 Z= 0.286 Chirality : 0.042 0.146 3056 Planarity : 0.003 0.046 3440 Dihedral : 6.216 57.111 2804 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.01 % Allowed : 16.76 % Favored : 81.23 % 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 (0.17), residues: 2420 helix: -0.20 (0.17), residues: 998 sheet: -0.05 (0.27), residues: 380 loop : -1.91 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 231 HIS 0.005 0.001 HIS B 129 PHE 0.020 0.001 PHE A 183 TYR 0.011 0.001 TYR D 206 ARG 0.003 0.000 ARG C 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 140 time to evaluate : 2.193 Fit side-chains revert: symmetry clash REVERT: A 490 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6811 (ptm) REVERT: A 651 ILE cc_start: 0.8214 (mm) cc_final: 0.7742 (mm) REVERT: B 71 LEU cc_start: 0.5864 (OUTLIER) cc_final: 0.5568 (mp) REVERT: B 187 LEU cc_start: 0.5917 (tp) cc_final: 0.5569 (tp) REVERT: B 644 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8150 (tt) REVERT: D 551 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: C 661 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.5794 (mp0) REVERT: C 666 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7113 (tm-30) outliers start: 43 outliers final: 29 residues processed: 175 average time/residue: 0.2875 time to fit residues: 81.1385 Evaluate side-chains 170 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 135 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 504 ASN Chi-restraints excluded: chain D residue 551 GLU Chi-restraints excluded: chain D residue 596 ASN Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 666 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 198 optimal weight: 0.0970 chunk 131 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 ASN ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20086 Z= 0.148 Angle : 0.470 7.457 27106 Z= 0.244 Chirality : 0.039 0.149 3056 Planarity : 0.003 0.050 3440 Dihedral : 5.406 49.693 2804 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.73 % Allowed : 17.37 % Favored : 80.91 % 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: -1.00 (0.17), residues: 2420 helix: 0.12 (0.17), residues: 994 sheet: 0.05 (0.28), residues: 370 loop : -1.67 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 309 HIS 0.005 0.001 HIS B 129 PHE 0.020 0.001 PHE A 183 TYR 0.014 0.001 TYR B 344 ARG 0.003 0.000 ARG C 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 152 time to evaluate : 2.481 Fit side-chains revert: symmetry clash REVERT: A 141 MET cc_start: 0.7379 (ptp) cc_final: 0.7151 (mtp) REVERT: A 651 ILE cc_start: 0.8086 (mm) cc_final: 0.7688 (mm) REVERT: B 71 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5509 (mp) REVERT: B 187 LEU cc_start: 0.5950 (tp) cc_final: 0.5647 (tp) REVERT: B 352 MET cc_start: 0.3072 (mmm) cc_final: 0.2212 (ptp) REVERT: D 551 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: D 622 LEU cc_start: 0.7483 (mm) cc_final: 0.7106 (mm) REVERT: C 292 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8030 (ptp) REVERT: C 666 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7015 (tm-30) outliers start: 37 outliers final: 22 residues processed: 183 average time/residue: 0.3083 time to fit residues: 90.0587 Evaluate side-chains 167 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 551 GLU Chi-restraints excluded: chain D residue 596 ASN Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 666 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.8980 chunk 93 optimal weight: 0.2980 chunk 140 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 160 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 184 optimal weight: 20.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20086 Z= 0.148 Angle : 0.473 9.456 27106 Z= 0.243 Chirality : 0.040 0.192 3056 Planarity : 0.003 0.052 3440 Dihedral : 5.238 58.458 2804 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.73 % Allowed : 17.88 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.17), residues: 2420 helix: 0.18 (0.17), residues: 996 sheet: 0.27 (0.28), residues: 380 loop : -1.64 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 585 HIS 0.004 0.001 HIS B 129 PHE 0.020 0.001 PHE A 183 TYR 0.029 0.001 TYR B 344 ARG 0.003 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 2.215 Fit side-chains REVERT: A 141 MET cc_start: 0.7335 (ptp) cc_final: 0.7134 (mtp) REVERT: A 651 ILE cc_start: 0.8095 (mm) cc_final: 0.7695 (mm) REVERT: B 71 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5516 (mp) REVERT: B 187 LEU cc_start: 0.5942 (tp) cc_final: 0.5630 (tp) REVERT: B 352 MET cc_start: 0.3142 (mmm) cc_final: 0.2254 (ptp) REVERT: D 551 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: D 622 LEU cc_start: 0.7461 (mm) cc_final: 0.7114 (mm) REVERT: C 666 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7043 (tm-30) outliers start: 37 outliers final: 25 residues processed: 178 average time/residue: 0.2772 time to fit residues: 80.2267 Evaluate side-chains 171 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 551 GLU Chi-restraints excluded: chain D residue 596 ASN Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 666 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.7980 chunk 225 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 219 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 198 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 218 optimal weight: 0.7980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20086 Z= 0.290 Angle : 0.555 8.005 27106 Z= 0.286 Chirality : 0.042 0.200 3056 Planarity : 0.003 0.053 3440 Dihedral : 5.701 59.342 2804 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.15 % Allowed : 17.74 % Favored : 80.11 % 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: -1.08 (0.17), residues: 2420 helix: 0.03 (0.17), residues: 996 sheet: 0.18 (0.28), residues: 380 loop : -1.79 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 585 HIS 0.005 0.001 HIS A 620 PHE 0.021 0.001 PHE A 183 TYR 0.022 0.001 TYR B 344 ARG 0.004 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 144 time to evaluate : 2.390 Fit side-chains revert: symmetry clash REVERT: A 141 MET cc_start: 0.7406 (ptp) cc_final: 0.7186 (mtp) REVERT: A 651 ILE cc_start: 0.8185 (mm) cc_final: 0.7712 (mm) REVERT: B 71 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5643 (mp) REVERT: B 187 LEU cc_start: 0.5882 (tp) cc_final: 0.5529 (tp) REVERT: B 352 MET cc_start: 0.3187 (mmm) cc_final: 0.2239 (ptp) REVERT: B 677 MET cc_start: 0.8172 (tpp) cc_final: 0.7460 (tpp) REVERT: D 301 MET cc_start: 0.6797 (mmm) cc_final: 0.6322 (mmm) REVERT: D 551 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: D 583 MET cc_start: 0.6792 (tpt) cc_final: 0.6546 (tpt) REVERT: D 622 LEU cc_start: 0.7557 (mm) cc_final: 0.7202 (mm) REVERT: C 490 MET cc_start: 0.7633 (mpt) cc_final: 0.7366 (mpp) REVERT: C 661 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.5973 (mp0) REVERT: C 666 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7059 (tm-30) outliers start: 46 outliers final: 32 residues processed: 180 average time/residue: 0.2742 time to fit residues: 80.9789 Evaluate side-chains 179 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 143 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 504 ASN Chi-restraints excluded: chain D residue 551 GLU Chi-restraints excluded: chain D residue 596 ASN Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 609 MET Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 666 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 243 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN C 496 ASN ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 20086 Z= 0.400 Angle : 0.648 8.161 27106 Z= 0.333 Chirality : 0.045 0.205 3056 Planarity : 0.004 0.056 3440 Dihedral : 6.296 59.210 2804 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.05 % Allowed : 18.02 % Favored : 79.93 % 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: -1.48 (0.17), residues: 2420 helix: -0.24 (0.17), residues: 972 sheet: -0.08 (0.27), residues: 394 loop : -2.05 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 231 HIS 0.006 0.001 HIS A 620 PHE 0.026 0.002 PHE D 183 TYR 0.022 0.002 TYR B 344 ARG 0.004 0.001 ARG D 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 145 time to evaluate : 2.669 Fit side-chains REVERT: A 141 MET cc_start: 0.7449 (ptp) cc_final: 0.7188 (mtp) REVERT: B 187 LEU cc_start: 0.5938 (tp) cc_final: 0.5573 (tp) REVERT: D 301 MET cc_start: 0.6883 (mmm) cc_final: 0.6529 (mmm) REVERT: D 551 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: C 184 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8448 (mm) REVERT: C 666 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7176 (tm-30) outliers start: 44 outliers final: 33 residues processed: 181 average time/residue: 0.2810 time to fit residues: 82.6106 Evaluate side-chains 178 residues out of total 2146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 504 ASN Chi-restraints excluded: chain D residue 551 GLU Chi-restraints excluded: chain D residue 596 ASN Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 666 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 193 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.108276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.086424 restraints weight = 52037.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.087164 restraints weight = 39564.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.087778 restraints weight = 37255.643| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20086 Z= 0.127 Angle : 0.495 9.690 27106 Z= 0.252 Chirality : 0.040 0.199 3056 Planarity : 0.003 0.055 3440 Dihedral : 5.303 55.412 2804 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.49 % Allowed : 18.67 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2420 helix: 0.14 (0.17), residues: 994 sheet: 0.13 (0.28), residues: 370 loop : -1.71 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 585 HIS 0.005 0.001 HIS B 129 PHE 0.029 0.001 PHE D 183 TYR 0.021 0.001 TYR B 344 ARG 0.004 0.000 ARG C 692 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3053.05 seconds wall clock time: 56 minutes 47.57 seconds (3407.57 seconds total)