Starting phenix.real_space_refine on Tue Aug 6 16:08:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/08_2024/7oqh_12701.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/08_2024/7oqh_12701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/08_2024/7oqh_12701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/08_2024/7oqh_12701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/08_2024/7oqh_12701.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/08_2024/7oqh_12701.cif" } resolution = 3.32 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 5 5.21 5 S 54 5.16 5 C 10470 2.51 5 N 3042 2.21 5 O 3235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B GLU 430": "OE1" <-> "OE2" Residue "B ASP 440": "OD1" <-> "OD2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "D PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 267": "OD1" <-> "OD2" Residue "E GLU 389": "OE1" <-> "OE2" Residue "E GLU 390": "OE1" <-> "OE2" Residue "E PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 423": "OE1" <-> "OE2" Residue "E GLU 430": "OE1" <-> "OE2" Residue "E GLU 508": "OE1" <-> "OE2" Residue "F ASP 385": "OD1" <-> "OD2" Residue "F PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 440": "OD1" <-> "OD2" Residue "F TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16824 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2770 Classifications: {'peptide': 363} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2787 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2775 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2797 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 341} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2772 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2732 Classifications: {'peptide': 356} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.71, per 1000 atoms: 0.52 Number of scatterers: 16824 At special positions: 0 Unit cell: (147.882, 131.451, 103.069, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 18 15.00 Mg 5 11.99 O 3235 8.00 N 3042 7.00 C 10470 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: 6.20 Conformation dependent library (CDL) restraints added in 3.0 seconds 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4010 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 14 sheets defined 43.8% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 331 through 341 removed outlier: 3.736A pdb=" N ARG A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.504A pdb=" N VAL A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 432 removed outlier: 3.790A pdb=" N HIS A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.549A pdb=" N LYS A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 509 removed outlier: 3.796A pdb=" N THR A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.839A pdb=" N LEU A 545 " --> pdb=" O LYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 565 removed outlier: 4.140A pdb=" N LEU A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 582 through 592 removed outlier: 3.559A pdb=" N GLU A 586 " --> pdb=" O LYS A 582 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.862A pdb=" N LEU B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 374 Processing helix chain 'B' and resid 387 through 398 removed outlier: 3.875A pdb=" N THR B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 431 Processing helix chain 'B' and resid 441 through 453 removed outlier: 4.103A pdb=" N SER B 453 " --> pdb=" O TYR B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 469 Processing helix chain 'B' and resid 470 through 478 Processing helix chain 'B' and resid 500 through 510 removed outlier: 3.610A pdb=" N THR B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 527 Processing helix chain 'B' and resid 548 through 564 Processing helix chain 'B' and resid 566 through 581 removed outlier: 3.805A pdb=" N THR B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 592 Processing helix chain 'C' and resid 255 through 262 Processing helix chain 'C' and resid 334 through 341 Processing helix chain 'C' and resid 358 through 374 Processing helix chain 'C' and resid 387 through 398 removed outlier: 3.948A pdb=" N THR C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 431 removed outlier: 3.606A pdb=" N GLN C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 453 removed outlier: 3.529A pdb=" N SER C 453 " --> pdb=" O TYR C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 477 removed outlier: 3.652A pdb=" N LYS C 473 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 510 removed outlier: 3.914A pdb=" N THR C 504 " --> pdb=" O SER C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 526 Processing helix chain 'C' and resid 542 through 546 removed outlier: 4.034A pdb=" N LEU C 545 " --> pdb=" O LYS C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 564 removed outlier: 4.066A pdb=" N GLY C 564 " --> pdb=" O ARG C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 579 Processing helix chain 'C' and resid 582 through 592 Processing helix chain 'D' and resid 254 through 261 Processing helix chain 'D' and resid 332 through 341 Processing helix chain 'D' and resid 358 through 374 removed outlier: 3.593A pdb=" N ILE D 362 " --> pdb=" O GLY D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 398 removed outlier: 3.777A pdb=" N THR D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 431 removed outlier: 3.688A pdb=" N GLN D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 453 removed outlier: 3.965A pdb=" N SER D 453 " --> pdb=" O TYR D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 468 No H-bonds generated for 'chain 'D' and resid 466 through 468' Processing helix chain 'D' and resid 469 through 478 removed outlier: 3.600A pdb=" N LYS D 473 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 510 removed outlier: 3.781A pdb=" N THR D 504 " --> pdb=" O SER D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 527 removed outlier: 3.565A pdb=" N ARG D 527 " --> pdb=" O LYS D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 removed outlier: 4.087A pdb=" N LEU D 545 " --> pdb=" O LYS D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 565 removed outlier: 3.912A pdb=" N LEU D 565 " --> pdb=" O VAL D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 578 Processing helix chain 'D' and resid 583 through 592 removed outlier: 3.726A pdb=" N SER D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 262 Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 358 through 374 Processing helix chain 'E' and resid 387 through 398 removed outlier: 3.784A pdb=" N THR E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP E 393 " --> pdb=" O GLU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 432 Processing helix chain 'E' and resid 441 through 453 removed outlier: 3.799A pdb=" N SER E 453 " --> pdb=" O TYR E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 468 Processing helix chain 'E' and resid 469 through 477 removed outlier: 3.752A pdb=" N LYS E 473 " --> pdb=" O LEU E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 510 removed outlier: 3.746A pdb=" N THR E 504 " --> pdb=" O SER E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 526 Processing helix chain 'E' and resid 542 through 546 removed outlier: 3.839A pdb=" N LEU E 545 " --> pdb=" O LYS E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 565 removed outlier: 3.578A pdb=" N LEU E 565 " --> pdb=" O VAL E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 580 removed outlier: 4.032A pdb=" N ASP E 572 " --> pdb=" O HIS E 568 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS E 580 " --> pdb=" O SER E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 592 removed outlier: 3.583A pdb=" N SER E 592 " --> pdb=" O LEU E 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 262 Processing helix chain 'F' and resid 309 through 313 removed outlier: 3.693A pdb=" N LYS F 313 " --> pdb=" O GLU F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 341 removed outlier: 3.853A pdb=" N ARG F 335 " --> pdb=" O ARG F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 374 Processing helix chain 'F' and resid 387 through 398 removed outlier: 3.530A pdb=" N THR F 392 " --> pdb=" O PRO F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 431 removed outlier: 3.749A pdb=" N GLN F 431 " --> pdb=" O ARG F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 451 removed outlier: 3.574A pdb=" N LEU F 445 " --> pdb=" O SER F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 468 No H-bonds generated for 'chain 'F' and resid 466 through 468' Processing helix chain 'F' and resid 469 through 478 removed outlier: 3.871A pdb=" N LYS F 473 " --> pdb=" O LEU F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 510 Processing helix chain 'F' and resid 521 through 527 Processing helix chain 'F' and resid 548 through 564 Processing helix chain 'F' and resid 566 through 581 removed outlier: 3.783A pdb=" N THR F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 589 Processing sheet with id=AA1, first strand: chain 'A' and resid 251 through 253 removed outlier: 3.965A pdb=" N ALA A 227 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 323 removed outlier: 4.503A pdb=" N ILE A 343 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 401 through 403 removed outlier: 7.054A pdb=" N LEU A 379 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE A 403 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL A 381 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 436 " --> pdb=" O HIS A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 401 through 403 removed outlier: 7.054A pdb=" N LEU A 379 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE A 403 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL A 381 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 436 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA A 349 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA A 494 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 351 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ARG A 348 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU A 518 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU A 350 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU A 520 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL A 352 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N GLU A 517 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N ASN A 536 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS A 519 " --> pdb=" O ASP A 534 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 250 through 253 removed outlier: 3.561A pdb=" N ALA B 237 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY B 228 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA B 268 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE B 297 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR B 270 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 293 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 401 through 406 removed outlier: 6.731A pdb=" N LEU B 379 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE B 403 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL B 381 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N SER B 405 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU B 383 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N HIS B 378 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU B 438 " --> pdb=" O HIS B 378 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET B 380 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASP B 440 " --> pdb=" O MET B 380 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL B 382 " --> pdb=" O ASP B 440 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ALA B 349 " --> pdb=" O ALA B 492 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA B 494 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE B 351 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG B 348 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N LEU B 518 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 350 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU B 520 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 352 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N GLU B 517 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N ASN B 536 " --> pdb=" O GLU B 517 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS B 519 " --> pdb=" O ASP B 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 253 through 254 removed outlier: 4.222A pdb=" N GLY C 228 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA C 268 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE C 297 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR C 270 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 295 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 401 through 406 removed outlier: 3.575A pdb=" N ASP C 385 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N HIS C 378 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU C 438 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N MET C 380 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASP C 440 " --> pdb=" O MET C 380 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL C 382 " --> pdb=" O ASP C 440 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 493 " --> pdb=" O LEU C 439 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA C 349 " --> pdb=" O ALA C 492 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA C 494 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE C 351 " --> pdb=" O ALA C 494 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ARG C 348 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N LEU C 518 " --> pdb=" O ARG C 348 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 350 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU C 520 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL C 352 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N GLU C 517 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N ASN C 536 " --> pdb=" O GLU C 517 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYS C 519 " --> pdb=" O ASP C 534 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 238 through 240 removed outlier: 3.901A pdb=" N GLY D 228 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA D 268 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE D 297 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR D 270 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG D 293 " --> pdb=" O ALA D 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 401 through 406 removed outlier: 6.755A pdb=" N LEU D 379 " --> pdb=" O GLU D 401 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE D 403 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL D 381 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N SER D 405 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU D 383 " --> pdb=" O SER D 405 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL D 384 " --> pdb=" O ASP D 440 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR D 493 " --> pdb=" O LEU D 439 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA D 349 " --> pdb=" O ALA D 492 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA D 494 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE D 351 " --> pdb=" O ALA D 494 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG D 348 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LEU D 518 " --> pdb=" O ARG D 348 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU D 350 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU D 520 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL D 352 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 9.623A pdb=" N GLU D 517 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ASN D 536 " --> pdb=" O GLU D 517 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS D 519 " --> pdb=" O ASP D 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 251 through 254 removed outlier: 4.089A pdb=" N GLY E 228 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA E 227 " --> pdb=" O VAL E 269 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 401 through 406 removed outlier: 6.996A pdb=" N LEU E 379 " --> pdb=" O GLU E 401 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE E 403 " --> pdb=" O LEU E 379 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL E 381 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N SER E 405 " --> pdb=" O VAL E 381 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU E 383 " --> pdb=" O SER E 405 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL E 436 " --> pdb=" O HIS E 378 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 382 " --> pdb=" O LEU E 438 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL E 384 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL E 435 " --> pdb=" O THR E 489 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE E 491 " --> pdb=" O VAL E 435 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL E 437 " --> pdb=" O ILE E 491 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR E 493 " --> pdb=" O VAL E 437 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU E 439 " --> pdb=" O THR E 493 " (cutoff:3.500A) removed outlier: 9.504A pdb=" N MET E 495 " --> pdb=" O LEU E 439 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA E 349 " --> pdb=" O ALA E 492 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA E 494 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE E 351 " --> pdb=" O ALA E 494 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA E 516 " --> pdb=" O ARG E 348 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 289 through 290 removed outlier: 3.814A pdb=" N VAL F 251 " --> pdb=" O VAL F 239 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY F 228 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER F 296 " --> pdb=" O THR F 270 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 401 through 406 removed outlier: 6.810A pdb=" N LEU F 379 " --> pdb=" O GLU F 401 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE F 403 " --> pdb=" O LEU F 379 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL F 381 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N SER F 405 " --> pdb=" O VAL F 381 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU F 383 " --> pdb=" O SER F 405 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL F 384 " --> pdb=" O ASP F 440 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 439 " --> pdb=" O ILE F 491 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA F 492 " --> pdb=" O ALA F 349 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA F 516 " --> pdb=" O ARG F 348 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N GLU F 517 " --> pdb=" O ASN F 536 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ASN F 536 " --> pdb=" O GLU F 517 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS F 519 " --> pdb=" O ASP F 534 " (cutoff:3.500A) 703 hydrogen bonds defined for protein. 2034 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: 4.74 Time building geometry restraints manager: 6.81 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: 5732 1.34 - 1.46: 2062 1.46 - 1.57: 9154 1.57 - 1.69: 27 1.69 - 1.81: 101 Bond restraints: 17076 Sorted by residual: bond pdb=" CB PRO E 248 " pdb=" CG PRO E 248 " ideal model delta sigma weight residual 1.492 1.631 -0.139 5.00e-02 4.00e+02 7.69e+00 bond pdb=" C GLN E 224 " pdb=" N PRO E 225 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.19e+00 bond pdb=" N PRO E 248 " pdb=" CA PRO E 248 " ideal model delta sigma weight residual 1.473 1.461 0.011 8.50e-03 1.38e+04 1.83e+00 bond pdb=" CA ASP C 543 " pdb=" CB ASP C 543 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.68e-02 3.54e+03 1.20e+00 bond pdb=" C TYR F 318 " pdb=" N PRO F 319 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.92e-01 ... (remaining 17071 not shown) Histogram of bond angle deviations from ideal: 99.08 - 107.23: 722 107.23 - 115.37: 10614 115.37 - 123.52: 11332 123.52 - 131.66: 469 131.66 - 139.81: 22 Bond angle restraints: 23159 Sorted by residual: angle pdb=" CA PRO E 248 " pdb=" N PRO E 248 " pdb=" CD PRO E 248 " ideal model delta sigma weight residual 112.00 104.79 7.21 1.40e+00 5.10e-01 2.65e+01 angle pdb=" N TYR E 318 " pdb=" CA TYR E 318 " pdb=" C TYR E 318 " ideal model delta sigma weight residual 109.81 118.41 -8.60 2.21e+00 2.05e-01 1.51e+01 angle pdb=" C SER B 242 " pdb=" N GLY B 243 " pdb=" CA GLY B 243 " ideal model delta sigma weight residual 121.70 128.67 -6.97 1.80e+00 3.09e-01 1.50e+01 angle pdb=" C LEU E 317 " pdb=" N TYR E 318 " pdb=" CA TYR E 318 " ideal model delta sigma weight residual 121.80 131.16 -9.36 2.44e+00 1.68e-01 1.47e+01 angle pdb=" C LYS D 580 " pdb=" N THR D 581 " pdb=" CA THR D 581 " ideal model delta sigma weight residual 121.54 128.17 -6.63 1.91e+00 2.74e-01 1.21e+01 ... (remaining 23154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9529 17.98 - 35.97: 904 35.97 - 53.95: 205 53.95 - 71.93: 32 71.93 - 89.91: 17 Dihedral angle restraints: 10687 sinusoidal: 4479 harmonic: 6208 Sorted by residual: dihedral pdb=" CA TYR D 318 " pdb=" C TYR D 318 " pdb=" N PRO D 319 " pdb=" CA PRO D 319 " ideal model delta harmonic sigma weight residual 180.00 151.32 28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA TYR E 318 " pdb=" C TYR E 318 " pdb=" N PRO E 319 " pdb=" CA PRO E 319 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLN E 224 " pdb=" C GLN E 224 " pdb=" N PRO E 225 " pdb=" CA PRO E 225 " ideal model delta harmonic sigma weight residual 180.00 -159.48 -20.52 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 10684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2055 0.047 - 0.093: 492 0.093 - 0.140: 155 0.140 - 0.186: 5 0.186 - 0.232: 2 Chirality restraints: 2709 Sorted by residual: chirality pdb=" CA TYR D 318 " pdb=" N TYR D 318 " pdb=" C TYR D 318 " pdb=" CB TYR D 318 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA TYR E 318 " pdb=" N TYR E 318 " pdb=" C TYR E 318 " pdb=" CB TYR E 318 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CA PRO E 225 " pdb=" N PRO E 225 " pdb=" C PRO E 225 " pdb=" CB PRO E 225 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 2706 not shown) Planarity restraints: 3003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 536 " -0.056 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO B 537 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 537 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 537 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 308 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO B 309 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 309 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 309 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 548 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO C 549 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 549 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 549 " -0.030 5.00e-02 4.00e+02 ... (remaining 3000 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 151 2.55 - 3.14: 13346 3.14 - 3.73: 25644 3.73 - 4.31: 34974 4.31 - 4.90: 59588 Nonbonded interactions: 133703 Sorted by model distance: nonbonded pdb=" O2B ATP F 701 " pdb="MG MG F 702 " model vdw 1.967 2.170 nonbonded pdb=" O2B ATP D 701 " pdb="MG MG D 702 " model vdw 1.977 2.170 nonbonded pdb=" O2B ATP E 701 " pdb="MG MG E 702 " model vdw 1.978 2.170 nonbonded pdb=" O2G ATP B 701 " pdb="MG MG B 702 " model vdw 1.983 2.170 nonbonded pdb=" O2G ATP F 701 " pdb="MG MG F 702 " model vdw 2.007 2.170 ... (remaining 133698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 223 through 262 or (resid 263 and (name N or name CA or na \ me C or name O or name CB or name CG or name SD )) or resid 264 through 276 or r \ esid 288 through 330 or (resid 331 and (name N or name CA or name C or name O or \ name CB )) or resid 332 through 423 or (resid 424 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ )) or resid \ 425 through 455 or (resid 460 and (name N or name CA or name C or name O or nam \ e CB )) or resid 461 through 466 or (resid 467 and (name N or name CA or name C \ or name O or name CB or name OG1)) or resid 468 through 481 or (resid 482 and (n \ ame N or name CA or name C or name O or name CB or name CG1 or name CG2)) or res \ id 483 through 589)) selection = (chain 'B' and (resid 223 through 276 or resid 288 through 306 or (resid 307 thr \ ough 308 and (name N or name CA or name C or name O or name CB )) or resid 309 t \ hrough 330 or (resid 331 and (name N or name CA or name C or name O or name CB ) \ ) or resid 332 through 348 or (resid 349 and (name N or name CA or name C or nam \ e O )) or resid 350 through 360 or (resid 361 and (name N or name CA or name C o \ r name O or name CB or name OG1)) or resid 362 through 455 or (resid 460 and (na \ me N or name CA or name C or name O or name CB )) or resid 461 through 466 or (r \ esid 467 and (name N or name CA or name C or name O or name CB or name OG1)) or \ resid 468 through 481 or (resid 482 and (name N or name CA or name C or name O o \ r name CB or name CG1 or name CG2)) or resid 483 through 526 or (resid 527 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name N \ E or name CZ )) or resid 528 through 556 or (resid 557 and (name N or name CA or \ name C or name O or name CB )) or resid 558 through 589)) selection = (chain 'C' and (resid 223 through 262 or (resid 263 and (name N or name CA or na \ me C or name O or name CB or name CG or name SD )) or resid 264 through 276 or r \ esid 288 through 306 or (resid 307 through 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 through 330 or (resid 331 and (name N or na \ me CA or name C or name O or name CB )) or resid 332 through 348 or (resid 349 a \ nd (name N or name CA or name C or name O )) or resid 350 through 360 or (resid \ 361 and (name N or name CA or name C or name O or name CB or name OG1)) or resid \ 362 through 423 or (resid 424 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name NE or name CZ )) or resid 425 through 455 or \ (resid 460 and (name N or name CA or name C or name O or name CB )) or resid 461 \ through 481 or (resid 482 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2)) or resid 483 through 526 or (resid 527 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name NE or name \ CZ )) or resid 528 through 556 or (resid 557 and (name N or name CA or name C o \ r name O or name CB )) or resid 558 through 589)) selection = (chain 'D' and (resid 223 through 262 or (resid 263 and (name N or name CA or na \ me C or name O or name CB or name CG or name SD )) or resid 264 through 276 or r \ esid 288 through 306 or (resid 307 through 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 through 330 or (resid 331 and (name N or na \ me CA or name C or name O or name CB )) or resid 332 through 348 or (resid 349 a \ nd (name N or name CA or name C or name O )) or resid 350 through 360 or (resid \ 361 and (name N or name CA or name C or name O or name CB or name OG1)) or resid \ 362 through 423 or (resid 424 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name NE or name CZ )) or resid 425 through 455 or \ (resid 460 and (name N or name CA or name C or name O or name CB )) or resid 461 \ through 466 or (resid 467 and (name N or name CA or name C or name O or name CB \ or name OG1)) or resid 468 through 481 or (resid 482 and (name N or name CA or \ name C or name O or name CB or name CG1 or name CG2)) or resid 483 through 526 o \ r (resid 527 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE or name CZ )) or resid 528 through 556 or (resid 557 and (na \ me N or name CA or name C or name O or name CB )) or resid 558 through 589)) selection = (chain 'E' and (resid 223 through 262 or (resid 263 and (name N or name CA or na \ me C or name O or name CB or name CG or name SD )) or resid 264 through 276 or r \ esid 288 through 306 or (resid 307 through 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 through 348 or (resid 349 and (name N or na \ me CA or name C or name O )) or resid 350 through 360 or (resid 361 and (name N \ or name CA or name C or name O or name CB or name OG1)) or resid 362 through 455 \ or (resid 460 and (name N or name CA or name C or name O or name CB )) or resid \ 461 through 466 or (resid 467 and (name N or name CA or name C or name O or nam \ e CB or name OG1)) or resid 468 through 526 or (resid 527 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name NE or name CZ )) o \ r resid 528 through 556 or (resid 557 and (name N or name CA or name C or name O \ or name CB )) or resid 558 through 589)) selection = (chain 'F' and (resid 223 through 262 or (resid 263 and (name N or name CA or na \ me C or name O or name CB or name CG or name SD )) or resid 264 through 276 or r \ esid 288 through 306 or (resid 307 through 308 and (name N or name CA or name C \ or name O or name CB )) or resid 309 through 330 or (resid 331 and (name N or na \ me CA or name C or name O or name CB )) or resid 332 through 360 or (resid 361 a \ nd (name N or name CA or name C or name O or name CB or name OG1)) or resid 362 \ through 423 or (resid 424 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ )) or resid 425 through 466 or (resi \ d 467 and (name N or name CA or name C or name O or name CB or name OG1)) or res \ id 468 through 481 or (resid 482 and (name N or name CA or name C or name O or n \ ame CB or name CG1 or name CG2)) or resid 483 through 556 or (resid 557 and (nam \ e N or name CA or name C or name O or name CB )) or resid 558 through 589)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 42.750 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 0.139 17076 Z= 0.264 Angle : 0.621 9.361 23159 Z= 0.322 Chirality : 0.044 0.232 2709 Planarity : 0.005 0.084 3003 Dihedral : 14.789 89.914 6677 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.49 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % 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: -0.13 (0.19), residues: 2143 helix: 1.44 (0.18), residues: 844 sheet: -1.01 (0.28), residues: 350 loop : -1.10 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 556 PHE 0.012 0.001 PHE F 475 TYR 0.018 0.001 TYR E 318 ARG 0.007 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 TYR cc_start: 0.4436 (t80) cc_final: 0.4170 (t80) REVERT: A 260 LYS cc_start: 0.7544 (mptt) cc_final: 0.7016 (mmtt) REVERT: A 330 GLU cc_start: 0.6032 (mm-30) cc_final: 0.5828 (mm-30) REVERT: A 341 MET cc_start: 0.8107 (ttt) cc_final: 0.7819 (ttt) REVERT: A 577 GLN cc_start: 0.6792 (tm-30) cc_final: 0.6577 (tm-30) REVERT: B 257 MET cc_start: 0.6348 (ttt) cc_final: 0.5800 (ttt) REVERT: B 394 MET cc_start: 0.8981 (tpt) cc_final: 0.8671 (tpp) REVERT: B 575 MET cc_start: 0.7565 (mmm) cc_final: 0.7088 (tpp) REVERT: D 263 MET cc_start: 0.7456 (mmm) cc_final: 0.6765 (mtt) REVERT: D 444 ARG cc_start: 0.7935 (mmt-90) cc_final: 0.7642 (mmm-85) REVERT: D 556 HIS cc_start: 0.7670 (t70) cc_final: 0.7391 (t70) REVERT: D 580 LYS cc_start: 0.6598 (mmtt) cc_final: 0.5385 (tptt) REVERT: E 263 MET cc_start: 0.7631 (tpp) cc_final: 0.7400 (tpp) REVERT: E 264 ARG cc_start: 0.6597 (mmt-90) cc_final: 0.5984 (mmt-90) REVERT: E 394 MET cc_start: 0.8761 (tpt) cc_final: 0.8377 (tpt) REVERT: E 556 HIS cc_start: 0.8065 (t70) cc_final: 0.7838 (t70) REVERT: F 321 GLN cc_start: 0.7473 (mt0) cc_final: 0.7258 (mt0) REVERT: F 364 GLN cc_start: 0.7866 (mt0) cc_final: 0.7634 (mt0) REVERT: F 449 TYR cc_start: 0.8378 (m-80) cc_final: 0.8071 (m-10) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.3090 time to fit residues: 140.2553 Evaluate side-chains 225 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 168 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 195 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN E 249 HIS ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17076 Z= 0.272 Angle : 0.633 8.670 23159 Z= 0.323 Chirality : 0.046 0.258 2709 Planarity : 0.006 0.059 3003 Dihedral : 9.832 82.915 2574 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.20 % Allowed : 7.39 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.79 % 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: -0.28 (0.18), residues: 2143 helix: 1.28 (0.18), residues: 873 sheet: -0.93 (0.28), residues: 342 loop : -1.30 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 414 PHE 0.012 0.001 PHE B 407 TYR 0.015 0.001 TYR E 318 ARG 0.006 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 248 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.7477 (mptt) cc_final: 0.6899 (mmtp) REVERT: A 341 MET cc_start: 0.8097 (ttt) cc_final: 0.7844 (ttt) REVERT: A 395 GLN cc_start: 0.7800 (mt0) cc_final: 0.7539 (mp10) REVERT: A 577 GLN cc_start: 0.6884 (tm-30) cc_final: 0.6639 (tm-30) REVERT: B 257 MET cc_start: 0.6108 (ttt) cc_final: 0.5830 (ttt) REVERT: B 394 MET cc_start: 0.9026 (tpt) cc_final: 0.8751 (tpp) REVERT: B 575 MET cc_start: 0.7929 (mmm) cc_final: 0.7639 (tpp) REVERT: C 429 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8240 (t) REVERT: D 263 MET cc_start: 0.7680 (mmm) cc_final: 0.6866 (mtt) REVERT: D 580 LYS cc_start: 0.6668 (mmtt) cc_final: 0.5363 (tptt) REVERT: E 394 MET cc_start: 0.8719 (tpt) cc_final: 0.8378 (tpt) REVERT: F 364 GLN cc_start: 0.7907 (mt0) cc_final: 0.7646 (mt0) outliers start: 22 outliers final: 17 residues processed: 260 average time/residue: 0.2975 time to fit residues: 116.9061 Evaluate side-chains 251 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 233 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 441 SER Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 0.0470 chunk 60 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17076 Z= 0.217 Angle : 0.583 8.961 23159 Z= 0.297 Chirality : 0.044 0.250 2709 Planarity : 0.005 0.048 3003 Dihedral : 9.408 85.021 2574 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.64 % Allowed : 9.79 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % 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: -0.23 (0.19), residues: 2143 helix: 1.34 (0.18), residues: 875 sheet: -0.91 (0.29), residues: 332 loop : -1.30 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 414 PHE 0.012 0.001 PHE B 407 TYR 0.015 0.001 TYR B 244 ARG 0.005 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 247 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.7453 (mptt) cc_final: 0.6832 (mmtp) REVERT: A 341 MET cc_start: 0.7915 (ttt) cc_final: 0.7552 (ttt) REVERT: A 395 GLN cc_start: 0.7716 (mt0) cc_final: 0.7433 (mp10) REVERT: A 577 GLN cc_start: 0.6897 (tm-30) cc_final: 0.6664 (tm-30) REVERT: B 257 MET cc_start: 0.6183 (ttt) cc_final: 0.5873 (ttt) REVERT: B 394 MET cc_start: 0.8959 (tpt) cc_final: 0.8721 (tpp) REVERT: B 575 MET cc_start: 0.7921 (mmm) cc_final: 0.7587 (mpp) REVERT: C 429 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8104 (t) REVERT: D 263 MET cc_start: 0.7626 (mmm) cc_final: 0.6910 (mtt) REVERT: D 580 LYS cc_start: 0.6783 (mmtt) cc_final: 0.5347 (tptt) REVERT: E 394 MET cc_start: 0.8679 (tpt) cc_final: 0.8335 (tpt) REVERT: E 431 GLN cc_start: 0.7155 (mm-40) cc_final: 0.6884 (tp40) REVERT: F 364 GLN cc_start: 0.7911 (mt0) cc_final: 0.7679 (mt0) REVERT: F 517 GLU cc_start: 0.6004 (tt0) cc_final: 0.5789 (tt0) outliers start: 30 outliers final: 22 residues processed: 266 average time/residue: 0.2793 time to fit residues: 113.5850 Evaluate side-chains 260 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 237 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 196 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN C 536 ASN ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17076 Z= 0.371 Angle : 0.658 8.497 23159 Z= 0.335 Chirality : 0.047 0.249 2709 Planarity : 0.006 0.055 3003 Dihedral : 9.428 87.517 2574 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.70 % Allowed : 12.58 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % Twisted Proline : 0.79 % 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: -0.60 (0.18), residues: 2143 helix: 0.91 (0.17), residues: 876 sheet: -1.03 (0.29), residues: 326 loop : -1.40 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 414 PHE 0.018 0.002 PHE B 475 TYR 0.028 0.002 TYR B 244 ARG 0.004 0.001 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 253 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.7476 (mptt) cc_final: 0.6848 (mmtp) REVERT: A 341 MET cc_start: 0.7996 (ttt) cc_final: 0.7720 (ttt) REVERT: A 395 GLN cc_start: 0.7851 (mt0) cc_final: 0.7369 (mp10) REVERT: A 509 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6599 (mt-10) REVERT: A 577 GLN cc_start: 0.6915 (tm-30) cc_final: 0.6639 (tm-30) REVERT: B 257 MET cc_start: 0.6304 (ttt) cc_final: 0.6015 (ttt) REVERT: B 321 GLN cc_start: 0.6674 (mp10) cc_final: 0.6467 (mp10) REVERT: B 394 MET cc_start: 0.9068 (tpt) cc_final: 0.8801 (tpp) REVERT: B 575 MET cc_start: 0.7969 (mmm) cc_final: 0.7516 (mpp) REVERT: C 429 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8075 (t) REVERT: C 447 ARG cc_start: 0.8098 (mtm110) cc_final: 0.7821 (mtp180) REVERT: D 263 MET cc_start: 0.7920 (mmm) cc_final: 0.7389 (mtt) REVERT: D 495 MET cc_start: 0.8696 (mmm) cc_final: 0.8414 (mmm) REVERT: D 580 LYS cc_start: 0.6538 (mmtt) cc_final: 0.5021 (tptt) REVERT: E 526 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7797 (mp0) outliers start: 31 outliers final: 24 residues processed: 272 average time/residue: 0.2975 time to fit residues: 121.0512 Evaluate side-chains 266 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 240 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 5.9990 chunk 117 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 106 optimal weight: 0.0570 chunk 186 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN C 368 ASN E 261 ASN F 289 ASN F 431 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17076 Z= 0.205 Angle : 0.577 8.771 23159 Z= 0.294 Chirality : 0.044 0.253 2709 Planarity : 0.005 0.049 3003 Dihedral : 9.035 89.594 2574 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.13 % Allowed : 13.51 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % 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: -0.38 (0.19), residues: 2143 helix: 1.18 (0.18), residues: 876 sheet: -1.04 (0.29), residues: 332 loop : -1.31 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 414 PHE 0.009 0.001 PHE F 475 TYR 0.013 0.001 TYR E 318 ARG 0.004 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 247 time to evaluate : 2.042 Fit side-chains revert: symmetry clash REVERT: A 260 LYS cc_start: 0.7451 (mptt) cc_final: 0.6797 (mmtp) REVERT: A 341 MET cc_start: 0.7902 (ttt) cc_final: 0.7635 (ttt) REVERT: A 395 GLN cc_start: 0.8226 (mt0) cc_final: 0.7595 (mp10) REVERT: A 509 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6322 (mt-10) REVERT: A 577 GLN cc_start: 0.6667 (tm-30) cc_final: 0.6424 (tm-30) REVERT: B 257 MET cc_start: 0.6391 (ttt) cc_final: 0.6181 (ttt) REVERT: B 321 GLN cc_start: 0.6722 (mp10) cc_final: 0.6467 (mp10) REVERT: B 394 MET cc_start: 0.8968 (tpt) cc_final: 0.8733 (tpp) REVERT: B 430 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7126 (mt-10) REVERT: B 575 MET cc_start: 0.7866 (mmm) cc_final: 0.7626 (mpp) REVERT: C 429 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8010 (t) REVERT: C 447 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7666 (mtp180) REVERT: D 263 MET cc_start: 0.7829 (mmm) cc_final: 0.7261 (mtt) REVERT: D 580 LYS cc_start: 0.6629 (mmtt) cc_final: 0.5035 (tptt) REVERT: E 236 TYR cc_start: 0.5872 (m-80) cc_final: 0.5658 (m-80) REVERT: E 394 MET cc_start: 0.8431 (tpt) cc_final: 0.8146 (tpt) REVERT: F 517 GLU cc_start: 0.6177 (tt0) cc_final: 0.5834 (tt0) outliers start: 39 outliers final: 27 residues processed: 271 average time/residue: 0.2829 time to fit residues: 116.2760 Evaluate side-chains 260 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 232 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 556 HIS Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 1.9990 chunk 187 optimal weight: 0.4980 chunk 41 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 172 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 109 optimal weight: 0.0970 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN C 368 ASN E 261 ASN F 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17076 Z= 0.189 Angle : 0.564 8.776 23159 Z= 0.287 Chirality : 0.043 0.249 2709 Planarity : 0.005 0.049 3003 Dihedral : 8.801 88.370 2574 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.24 % Allowed : 14.22 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % 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: -0.27 (0.19), residues: 2143 helix: 1.30 (0.18), residues: 878 sheet: -1.01 (0.29), residues: 333 loop : -1.30 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 414 PHE 0.011 0.001 PHE B 510 TYR 0.014 0.001 TYR C 244 ARG 0.004 0.000 ARG C 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 248 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.7434 (mptt) cc_final: 0.6771 (mmtp) REVERT: A 341 MET cc_start: 0.7857 (ttt) cc_final: 0.7517 (ttt) REVERT: A 577 GLN cc_start: 0.6676 (tm-30) cc_final: 0.6403 (tm-30) REVERT: B 257 MET cc_start: 0.6428 (ttt) cc_final: 0.6170 (ttm) REVERT: B 321 GLN cc_start: 0.6684 (mp10) cc_final: 0.6458 (mp10) REVERT: B 394 MET cc_start: 0.8976 (tpt) cc_final: 0.8695 (tpp) REVERT: B 575 MET cc_start: 0.7836 (mmm) cc_final: 0.7543 (mpp) REVERT: C 429 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.7972 (t) REVERT: C 447 ARG cc_start: 0.7936 (mtm110) cc_final: 0.7688 (mtp180) REVERT: D 263 MET cc_start: 0.7698 (mmm) cc_final: 0.7119 (mtt) REVERT: D 444 ARG cc_start: 0.7921 (mmt-90) cc_final: 0.7654 (mmt90) REVERT: D 580 LYS cc_start: 0.6571 (mmtt) cc_final: 0.5042 (tptt) REVERT: E 230 LEU cc_start: 0.7234 (tt) cc_final: 0.7010 (tt) REVERT: E 236 TYR cc_start: 0.5872 (m-80) cc_final: 0.5665 (m-80) REVERT: E 263 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7615 (mtm) REVERT: E 394 MET cc_start: 0.8490 (tpt) cc_final: 0.8201 (tpt) REVERT: E 526 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: F 489 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7831 (t) REVERT: F 517 GLU cc_start: 0.6012 (tt0) cc_final: 0.5707 (tt0) outliers start: 41 outliers final: 26 residues processed: 278 average time/residue: 0.2826 time to fit residues: 119.0059 Evaluate side-chains 269 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 556 HIS Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 545 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 117 optimal weight: 0.0870 chunk 175 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 126 optimal weight: 0.0070 chunk 95 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 298 ASN C 368 ASN F 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17076 Z= 0.176 Angle : 0.567 13.256 23159 Z= 0.285 Chirality : 0.043 0.242 2709 Planarity : 0.005 0.049 3003 Dihedral : 8.590 88.925 2574 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.81 % Allowed : 15.21 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.30 % 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: -0.17 (0.19), residues: 2143 helix: 1.42 (0.18), residues: 879 sheet: -0.99 (0.29), residues: 333 loop : -1.27 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 414 PHE 0.028 0.001 PHE F 552 TYR 0.011 0.001 TYR E 318 ARG 0.004 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4286 Ramachandran restraints generated. 2143 Oldfield, 0 Emsley, 2143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 254 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 LYS cc_start: 0.7414 (mptt) cc_final: 0.6743 (mmtp) REVERT: A 341 MET cc_start: 0.7830 (ttt) cc_final: 0.7497 (ttt) REVERT: A 395 GLN cc_start: 0.8249 (mt0) cc_final: 0.7672 (mp10) REVERT: B 257 MET cc_start: 0.6375 (ttt) cc_final: 0.6119 (ttm) REVERT: B 321 GLN cc_start: 0.6448 (mp10) cc_final: 0.6226 (mp10) REVERT: B 394 MET cc_start: 0.8964 (tpt) cc_final: 0.8700 (tpp) REVERT: B 575 MET cc_start: 0.7905 (mmm) cc_final: 0.7595 (mpp) REVERT: C 429 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.7933 (t) REVERT: D 263 MET cc_start: 0.7686 (mmm) cc_final: 0.7119 (mtt) REVERT: D 422 ILE cc_start: 0.7934 (tp) cc_final: 0.7631 (tp) REVERT: D 580 LYS cc_start: 0.6455 (mmtt) cc_final: 0.5132 (tptt) REVERT: E 230 LEU cc_start: 0.7261 (tt) cc_final: 0.7059 (tt) REVERT: E 263 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7533 (mtm) REVERT: E 526 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: F 489 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7800 (t) outliers start: 33 outliers final: 24 residues processed: 277 average time/residue: 0.2779 time to fit residues: 116.7677 Evaluate side-chains 269 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 241 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 517 GLU Chi-restraints excluded: chain D residue 330 GLU Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 469 LEU Chi-restraints excluded: chain F residue 489 THR Chi-restraints excluded: chain F residue 544 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.0382 > 50: distance: 57 - 113: 35.157 distance: 88 - 94: 28.478 distance: 94 - 95: 10.917 distance: 94 - 100: 42.492 distance: 95 - 96: 39.594 distance: 95 - 98: 39.356 distance: 96 - 97: 69.395 distance: 96 - 101: 41.295 distance: 98 - 99: 41.068 distance: 99 - 100: 39.382 distance: 101 - 102: 57.295 distance: 102 - 103: 40.386 distance: 102 - 105: 57.539 distance: 103 - 104: 39.364 distance: 103 - 106: 38.775 distance: 106 - 107: 58.865 distance: 107 - 108: 44.065 distance: 107 - 110: 16.876 distance: 108 - 113: 68.088 distance: 115 - 121: 17.341 distance: 117 - 118: 41.016 distance: 118 - 119: 35.843 distance: 118 - 120: 10.241 distance: 121 - 122: 15.763 distance: 122 - 123: 41.757 distance: 123 - 124: 4.668 distance: 123 - 128: 9.550 distance: 125 - 127: 11.892 distance: 128 - 129: 47.141 distance: 129 - 130: 36.371 distance: 129 - 132: 41.734 distance: 130 - 131: 41.148 distance: 130 - 136: 56.753 distance: 132 - 133: 39.997 distance: 133 - 134: 21.096 distance: 133 - 135: 35.914 distance: 136 - 142: 22.396 distance: 137 - 138: 39.732 distance: 138 - 143: 39.493 distance: 141 - 142: 23.849 distance: 143 - 144: 11.737 distance: 144 - 145: 27.829 distance: 144 - 147: 10.636 distance: 145 - 146: 37.863 distance: 145 - 149: 53.655 distance: 147 - 148: 69.692 distance: 149 - 150: 56.147 distance: 150 - 151: 40.180 distance: 151 - 153: 14.448 distance: 153 - 154: 23.127 distance: 154 - 155: 8.332 distance: 154 - 157: 6.626 distance: 155 - 160: 35.024 distance: 157 - 158: 30.157 distance: 157 - 159: 11.128