Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 05:17:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/04_2023/7oqh_12701_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/04_2023/7oqh_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_12701/04_2023/7oqh_12701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/04_2023/7oqh_12701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/04_2023/7oqh_12701_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqh_12701/04_2023/7oqh_12701_updated.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 9.35, per 1000 atoms: 0.56 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: 6.74 Conformation dependent library (CDL) restraints added in 2.6 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... running ksdssp... Secondary structure from input PDB file: 81 helices and 12 sheets defined 37.5% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 255 through 261 Processing helix chain 'A' and resid 332 through 340 Processing helix chain 'A' and resid 359 through 373 Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 411 through 431 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 442 through 452 Processing helix chain 'A' and resid 467 through 478 Proline residue: A 471 - end of helix Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 523 through 526 No H-bonds generated for 'chain 'A' and resid 523 through 526' Processing helix chain 'A' and resid 549 through 564 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 583 through 591 Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.862A pdb=" N LEU B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 373 Processing helix chain 'B' and resid 388 through 397 removed outlier: 3.875A pdb=" N THR B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 431 Processing helix chain 'B' and resid 442 through 452 Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 471 through 478 Processing helix chain 'B' and resid 501 through 510 Processing helix chain 'B' and resid 522 through 526 Processing helix chain 'B' and resid 549 through 563 Processing helix chain 'B' and resid 567 through 580 Processing helix chain 'B' and resid 583 through 591 Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 359 through 373 Processing helix chain 'C' and resid 388 through 397 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 411 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 442 through 452 Processing helix chain 'C' and resid 469 through 478 removed outlier: 3.652A pdb=" N LYS C 473 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 509 Processing helix chain 'C' and resid 522 through 526 Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 549 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 567 through 580 removed outlier: 4.402A pdb=" N LYS C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 591 Processing helix chain 'D' and resid 255 through 260 Processing helix chain 'D' and resid 333 through 340 Processing helix chain 'D' and resid 359 through 373 Processing helix chain 'D' and resid 388 through 397 removed outlier: 3.777A pdb=" N THR D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 430 Processing helix chain 'D' and resid 442 through 452 Processing helix chain 'D' and resid 467 through 478 Proline residue: D 471 - end of helix Processing helix chain 'D' and resid 501 through 509 Processing helix chain 'D' and resid 522 through 526 Processing helix chain 'D' and resid 543 through 545 No H-bonds generated for 'chain 'D' and resid 543 through 545' Processing helix chain 'D' and resid 549 through 564 Processing helix chain 'D' and resid 567 through 577 Processing helix chain 'D' and resid 584 through 591 Processing helix chain 'E' and resid 255 through 261 Processing helix chain 'E' and resid 336 through 339 No H-bonds generated for 'chain 'E' and resid 336 through 339' Processing helix chain 'E' and resid 359 through 373 Processing helix chain 'E' and resid 388 through 397 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 411 through 431 Processing helix chain 'E' and resid 442 through 452 Processing helix chain 'E' and resid 466 through 468 No H-bonds generated for 'chain 'E' and resid 466 through 468' Processing helix chain 'E' and resid 470 through 478 Processing helix chain 'E' and resid 501 through 510 Processing helix chain 'E' and resid 522 through 527 removed outlier: 4.086A pdb=" N ARG E 527 " --> pdb=" O LYS E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 545 No H-bonds generated for 'chain 'E' and resid 543 through 545' Processing helix chain 'E' and resid 549 through 564 Processing helix chain 'E' and resid 567 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 585 through 591 Processing helix chain 'F' and resid 255 through 261 Processing helix chain 'F' and resid 310 through 312 No H-bonds generated for 'chain 'F' and resid 310 through 312' Processing helix chain 'F' and resid 332 through 340 Processing helix chain 'F' and resid 359 through 373 Processing helix chain 'F' and resid 388 through 397 removed outlier: 3.530A pdb=" N THR F 392 " --> pdb=" O PRO F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 430 Processing helix chain 'F' and resid 442 through 450 Processing helix chain 'F' and resid 461 through 463 No H-bonds generated for 'chain 'F' and resid 461 through 463' Processing helix chain 'F' and resid 467 through 477 Proline residue: F 471 - end of helix Processing helix chain 'F' and resid 501 through 509 Processing helix chain 'F' and resid 522 through 526 Processing helix chain 'F' and resid 549 through 563 Processing helix chain 'F' and resid 567 through 580 Processing helix chain 'F' and resid 583 through 588 Processing sheet with id= A, first strand: chain 'A' and resid 229 through 231 Processing sheet with id= B, first strand: chain 'A' and resid 516 through 519 removed outlier: 8.177A pdb=" N ALA A 349 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 490 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE A 351 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA A 492 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N SER A 353 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ALA A 494 " --> pdb=" O SER A 353 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 435 " --> pdb=" O THR A 489 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE A 491 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 437 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N THR A 493 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU A 439 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N MET A 495 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N HIS A 378 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU A 438 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET A 380 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU A 401 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU A 383 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 403 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing sheet with id= C, 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: 6.889A pdb=" N ALA B 272 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU B 294 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 516 through 519 removed outlier: 3.642A pdb=" N ALA B 516 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ALA B 349 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE B 490 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE B 351 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA B 492 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER B 353 " --> pdb=" O ALA B 492 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA B 494 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B 435 " --> pdb=" O THR B 489 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE B 491 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 437 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N THR B 493 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU B 439 " --> pdb=" O THR B 493 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N MET B 495 " --> pdb=" O LEU B 439 " (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: 6.707A pdb=" N GLU B 401 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU B 383 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 403 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 228 through 231 removed outlier: 4.222A pdb=" N GLY C 228 " --> pdb=" O ARG C 240 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 516 through 520 removed outlier: 3.991A pdb=" N ALA C 516 " --> pdb=" O ARG C 348 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA C 349 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE C 490 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE C 351 " --> pdb=" O ILE C 490 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA C 492 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N SER C 353 " --> pdb=" O ALA C 492 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA C 494 " --> pdb=" O SER C 353 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C 435 " --> pdb=" O THR C 489 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE C 491 " --> pdb=" O VAL C 435 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 437 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR C 493 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU C 439 " --> pdb=" O THR C 493 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N MET C 495 " --> pdb=" O LEU C 439 " (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: 6.774A pdb=" N GLU C 401 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU C 383 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 403 " --> pdb=" O LEU C 383 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 237 through 240 removed outlier: 3.901A pdb=" N GLY D 228 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA D 272 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU D 294 " --> pdb=" O ALA D 272 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 516 through 520 removed outlier: 3.761A pdb=" N ALA D 516 " --> pdb=" O ARG D 348 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA D 349 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE D 490 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE D 351 " --> pdb=" O ILE D 490 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA D 492 " --> pdb=" O ILE D 351 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N SER D 353 " --> pdb=" O ALA D 492 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA D 494 " --> pdb=" O SER D 353 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR D 493 " --> pdb=" O LEU D 439 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N HIS D 378 " --> pdb=" O VAL D 436 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU D 438 " --> pdb=" O HIS D 378 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N MET D 380 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ASP D 440 " --> pdb=" O MET D 380 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL D 382 " --> pdb=" O ASP D 440 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU D 401 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU D 383 " --> pdb=" O GLU D 401 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE D 403 " --> pdb=" O LEU D 383 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 227 through 231 removed outlier: 4.089A pdb=" N GLY E 228 " --> pdb=" O ARG E 240 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 516 through 520 removed outlier: 3.897A pdb=" N ALA E 516 " --> pdb=" O ARG E 348 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ALA E 349 " --> pdb=" O LEU E 488 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE E 490 " --> pdb=" O ALA E 349 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ILE E 351 " --> pdb=" O ILE E 490 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA E 492 " --> pdb=" O ILE E 351 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N SER E 353 " --> pdb=" O ALA E 492 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA E 494 " --> pdb=" O SER E 353 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR E 493 " --> pdb=" O LEU E 439 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N HIS E 378 " --> pdb=" O VAL E 436 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU E 438 " --> pdb=" O HIS E 378 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N MET E 380 " --> pdb=" O LEU E 438 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP E 440 " --> pdb=" O MET E 380 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL E 382 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU E 401 " --> pdb=" O VAL E 381 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU E 383 " --> pdb=" O GLU E 401 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE E 403 " --> pdb=" O LEU E 383 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 268 through 270 removed outlier: 4.112A pdb=" N GLY F 228 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL F 251 " --> pdb=" O VAL F 239 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 516 through 519 removed outlier: 3.728A pdb=" N ALA F 516 " --> pdb=" O ARG F 348 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA F 349 " --> pdb=" O LEU F 488 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE F 490 " --> pdb=" O ALA F 349 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE F 351 " --> pdb=" O ILE F 490 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA F 492 " --> pdb=" O ILE F 351 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER F 353 " --> pdb=" O ALA F 492 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA F 494 " --> pdb=" O SER F 353 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 439 " --> pdb=" O ILE F 491 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N HIS F 378 " --> pdb=" O VAL F 436 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU F 438 " --> pdb=" O HIS F 378 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N MET F 380 " --> pdb=" O LEU F 438 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ASP F 440 " --> pdb=" O MET F 380 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL F 382 " --> pdb=" O ASP F 440 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLU F 401 " --> pdb=" O VAL F 381 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LEU F 383 " --> pdb=" O GLU F 401 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE F 403 " --> pdb=" O LEU F 383 " (cutoff:3.500A) 554 hydrogen bonds defined for protein. 1599 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: 4.92 Time building geometry restraints manager: 7.26 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: 9483 17.98 - 35.97: 844 35.97 - 53.95: 147 53.95 - 71.93: 15 71.93 - 89.91: 12 Dihedral angle restraints: 10501 sinusoidal: 4293 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 10498 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: 161 2.55 - 3.14: 13442 3.14 - 3.73: 25791 3.73 - 4.31: 35223 4.31 - 4.90: 59646 Nonbonded interactions: 134263 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 134258 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 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.880 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 44.430 Find NCS groups from input model: 1.500 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.010 ------------------------------------------------------------------------------- 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= 0.269 Angle : 0.621 9.361 23159 Z= 0.322 Chirality : 0.044 0.232 2709 Planarity : 0.005 0.084 3003 Dihedral : 13.628 89.914 6491 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 % 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 *********************** 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 : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.3034 time to fit residues: 136.5975 Evaluate side-chains 223 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.867 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7271 ------------------------------------------------------------------------------- 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: 7.9990 chunk 162 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 17076 Z= 0.404 Angle : 0.673 9.039 23159 Z= 0.340 Chirality : 0.047 0.253 2709 Planarity : 0.006 0.063 3003 Dihedral : 5.147 59.301 2388 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.95 % Favored : 93.00 % Rotamer Outliers : 1.48 % 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: -0.49 (0.18), residues: 2143 helix: 1.08 (0.18), residues: 843 sheet: -1.00 (0.30), residues: 314 loop : -1.32 (0.20), residues: 986 *********************** 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 274 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 247 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 20 residues processed: 261 average time/residue: 0.2979 time to fit residues: 116.2978 Evaluate side-chains 252 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 232 time to evaluate : 1.958 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1887 time to fit residues: 9.2301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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: 68.9797 > 50: distance: 92 - 97: 30.507 distance: 97 - 98: 18.464 distance: 98 - 99: 22.193 distance: 98 - 101: 44.660 distance: 99 - 100: 38.697 distance: 99 - 108: 58.055 distance: 101 - 102: 16.560 distance: 102 - 103: 42.564 distance: 102 - 104: 25.134 distance: 103 - 105: 12.240 distance: 105 - 107: 58.031 distance: 108 - 109: 16.235 distance: 108 - 114: 17.989 distance: 109 - 110: 39.297 distance: 110 - 115: 40.684 distance: 115 - 116: 40.006 distance: 116 - 117: 28.308 distance: 116 - 119: 40.396 distance: 117 - 118: 48.479 distance: 117 - 120: 12.189 distance: 121 - 122: 18.400 distance: 121 - 124: 14.879 distance: 122 - 123: 21.746 distance: 122 - 127: 18.565 distance: 124 - 125: 5.677 distance: 124 - 126: 21.675 distance: 127 - 128: 35.588 distance: 128 - 129: 13.397 distance: 128 - 131: 3.921 distance: 129 - 130: 3.947 distance: 129 - 135: 22.104 distance: 131 - 132: 28.309 distance: 132 - 133: 32.022 distance: 132 - 134: 51.056 distance: 135 - 136: 25.413 distance: 136 - 137: 22.564 distance: 136 - 139: 21.923 distance: 137 - 142: 41.555 distance: 139 - 140: 22.635 distance: 139 - 141: 35.914 distance: 142 - 143: 40.799 distance: 143 - 144: 40.232 distance: 143 - 146: 21.349 distance: 144 - 145: 13.420 distance: 144 - 150: 43.776 distance: 146 - 147: 46.467 distance: 147 - 149: 56.680 distance: 150 - 151: 39.212 distance: 151 - 152: 6.971 distance: 151 - 154: 40.327 distance: 152 - 153: 34.748 distance: 152 - 157: 24.328 distance: 157 - 158: 11.347 distance: 158 - 159: 39.994 distance: 159 - 160: 41.035 distance: 159 - 163: 39.444 distance: 161 - 162: 41.191 distance: 165 - 166: 37.390 distance: 165 - 167: 34.139