Starting phenix.real_space_refine (version: dev) on Sat Feb 25 04:07:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip2_9698/02_2023/6ip2_9698_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip2_9698/02_2023/6ip2_9698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip2_9698/02_2023/6ip2_9698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip2_9698/02_2023/6ip2_9698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip2_9698/02_2023/6ip2_9698_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip2_9698/02_2023/6ip2_9698_updated.pdb" } resolution = 3.7 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= 0.001 sd= 0.020 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 Process input model Symmetric amino acids flipped Residue "B TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 24660 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 11, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 486} Chain: "C" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 493} Chain: "D" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 493} Chain: "E" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 492} Chain: "F" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 6, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 491} Chain: "A" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4048 Classifications: {'peptide': 520} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 493} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.17, per 1000 atoms: 0.53 Number of scatterers: 24660 At special positions: 0 Unit cell: (143.719, 141.106, 112.362, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 P 36 15.00 O 4698 8.00 N 4302 7.00 C 15486 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: 10.59 Conformation dependent library (CDL) restraints added in 3.6 seconds 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5772 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 137 helices and 15 sheets defined 35.2% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'B' and resid 223 through 230 removed outlier: 3.836A pdb=" N PHE B 227 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N SER B 228 " --> pdb=" O LYS B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 275 removed outlier: 3.520A pdb=" N GLN B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 299 through 302 No H-bonds generated for 'chain 'B' and resid 299 through 302' Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 349 through 357 removed outlier: 3.656A pdb=" N SER B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 378 No H-bonds generated for 'chain 'B' and resid 376 through 378' Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.817A pdb=" N HIS B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 432 removed outlier: 4.178A pdb=" N VAL B 431 " --> pdb=" O LYS B 427 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 432 " --> pdb=" O GLU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 454 removed outlier: 3.560A pdb=" N GLY B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 removed outlier: 3.613A pdb=" N ALA B 482 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 530 removed outlier: 4.659A pdb=" N ASP B 520 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 558 removed outlier: 3.540A pdb=" N ALA B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 592 removed outlier: 4.091A pdb=" N LYS B 587 " --> pdb=" O GLN B 583 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 589 " --> pdb=" O MET B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 608 No H-bonds generated for 'chain 'B' and resid 605 through 608' Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'B' and resid 649 through 654 removed outlier: 3.743A pdb=" N GLU B 654 " --> pdb=" O ASP B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 683 removed outlier: 3.987A pdb=" N LEU B 682 " --> pdb=" O GLU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 698 removed outlier: 3.762A pdb=" N GLN B 697 " --> pdb=" O THR B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 718 removed outlier: 3.771A pdb=" N GLU B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 729 No H-bonds generated for 'chain 'B' and resid 726 through 729' Processing helix chain 'C' and resid 224 through 227 No H-bonds generated for 'chain 'C' and resid 224 through 227' Processing helix chain 'C' and resid 231 through 234 No H-bonds generated for 'chain 'C' and resid 231 through 234' Processing helix chain 'C' and resid 244 through 247 No H-bonds generated for 'chain 'C' and resid 244 through 247' Processing helix chain 'C' and resid 268 through 271 No H-bonds generated for 'chain 'C' and resid 268 through 271' Processing helix chain 'C' and resid 289 through 292 removed outlier: 4.057A pdb=" N ASN C 292 " --> pdb=" O GLU C 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 292' Processing helix chain 'C' and resid 297 through 304 removed outlier: 3.741A pdb=" N ALA C 300 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN C 301 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG C 303 " --> pdb=" O ALA C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 312 removed outlier: 4.232A pdb=" N GLU C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.661A pdb=" N LEU C 354 " --> pdb=" O VAL C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 350 through 354' Processing helix chain 'C' and resid 400 through 413 removed outlier: 4.097A pdb=" N LEU C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 412 " --> pdb=" O HIS C 408 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 432 removed outlier: 4.042A pdb=" N VAL C 431 " --> pdb=" O LYS C 427 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU C 432 " --> pdb=" O GLU C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 456 removed outlier: 3.535A pdb=" N GLY C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN C 454 " --> pdb=" O SER C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 480 No H-bonds generated for 'chain 'C' and resid 477 through 480' Processing helix chain 'C' and resid 512 through 530 removed outlier: 4.552A pdb=" N VAL C 517 " --> pdb=" O PRO C 513 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP C 520 " --> pdb=" O ARG C 516 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 560 removed outlier: 3.574A pdb=" N SER C 560 " --> pdb=" O ILE C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 572 No H-bonds generated for 'chain 'C' and resid 570 through 572' Processing helix chain 'C' and resid 578 through 592 removed outlier: 3.882A pdb=" N CYS C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 608 No H-bonds generated for 'chain 'C' and resid 605 through 608' Processing helix chain 'C' and resid 620 through 624 Processing helix chain 'C' and resid 649 through 654 Processing helix chain 'C' and resid 673 through 683 removed outlier: 3.524A pdb=" N LEU C 682 " --> pdb=" O GLU C 678 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 683 " --> pdb=" O ALA C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 697 Processing helix chain 'C' and resid 707 through 718 removed outlier: 3.739A pdb=" N GLU C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 734 removed outlier: 4.334A pdb=" N ALA C 731 " --> pdb=" O ARG C 727 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG C 734 " --> pdb=" O LEU C 730 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 227 No H-bonds generated for 'chain 'D' and resid 224 through 227' Processing helix chain 'D' and resid 241 through 243 No H-bonds generated for 'chain 'D' and resid 241 through 243' Processing helix chain 'D' and resid 245 through 248 No H-bonds generated for 'chain 'D' and resid 245 through 248' Processing helix chain 'D' and resid 266 through 272 removed outlier: 3.694A pdb=" N ALA D 270 " --> pdb=" O LYS D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 303 removed outlier: 3.774A pdb=" N ASN D 301 " --> pdb=" O SER D 298 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG D 303 " --> pdb=" O ALA D 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 298 through 303' Processing helix chain 'D' and resid 307 through 313 removed outlier: 3.636A pdb=" N GLU D 311 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 307 through 313' Processing helix chain 'D' and resid 349 through 352 No H-bonds generated for 'chain 'D' and resid 349 through 352' Processing helix chain 'D' and resid 376 through 378 No H-bonds generated for 'chain 'D' and resid 376 through 378' Processing helix chain 'D' and resid 381 through 383 No H-bonds generated for 'chain 'D' and resid 381 through 383' Processing helix chain 'D' and resid 400 through 410 removed outlier: 3.797A pdb=" N LEU D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN D 405 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 431 No H-bonds generated for 'chain 'D' and resid 428 through 431' Processing helix chain 'D' and resid 438 through 454 removed outlier: 3.601A pdb=" N ASN D 454 " --> pdb=" O SER D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 483 Processing helix chain 'D' and resid 499 through 501 No H-bonds generated for 'chain 'D' and resid 499 through 501' Processing helix chain 'D' and resid 512 through 529 removed outlier: 4.084A pdb=" N VAL D 517 " --> pdb=" O PRO D 513 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP D 520 " --> pdb=" O ARG D 516 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 524 " --> pdb=" O ASP D 520 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLN D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 558 Processing helix chain 'D' and resid 570 through 573 Processing helix chain 'D' and resid 578 through 591 removed outlier: 3.800A pdb=" N CYS D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 584 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS D 587 " --> pdb=" O GLN D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 608 No H-bonds generated for 'chain 'D' and resid 605 through 608' Processing helix chain 'D' and resid 620 through 623 No H-bonds generated for 'chain 'D' and resid 620 through 623' Processing helix chain 'D' and resid 649 through 652 No H-bonds generated for 'chain 'D' and resid 649 through 652' Processing helix chain 'D' and resid 673 through 683 removed outlier: 3.523A pdb=" N LEU D 683 " --> pdb=" O ALA D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 698 removed outlier: 3.535A pdb=" N THR D 693 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE D 694 " --> pdb=" O GLU D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 717 Processing helix chain 'D' and resid 727 through 734 removed outlier: 3.911A pdb=" N ARG D 734 " --> pdb=" O LEU D 730 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 227 No H-bonds generated for 'chain 'E' and resid 224 through 227' Processing helix chain 'E' and resid 229 through 233 removed outlier: 3.564A pdb=" N ARG E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 229 through 233' Processing helix chain 'E' and resid 243 through 247 Processing helix chain 'E' and resid 266 through 272 removed outlier: 3.537A pdb=" N ALA E 270 " --> pdb=" O LYS E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 307 through 312 Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 348 through 358 removed outlier: 3.673A pdb=" N ASN E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE E 358 " --> pdb=" O LEU E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 410 removed outlier: 3.549A pdb=" N ILE E 406 " --> pdb=" O GLY E 402 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS E 408 " --> pdb=" O LEU E 404 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE E 409 " --> pdb=" O GLN E 405 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS E 410 " --> pdb=" O ILE E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 432 Processing helix chain 'E' and resid 438 through 454 removed outlier: 3.686A pdb=" N VAL E 445 " --> pdb=" O LEU E 441 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA E 447 " --> pdb=" O GLY E 443 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER E 450 " --> pdb=" O ARG E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 483 removed outlier: 3.572A pdb=" N ALA E 482 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 501 No H-bonds generated for 'chain 'E' and resid 499 through 501' Processing helix chain 'E' and resid 512 through 530 removed outlier: 3.765A pdb=" N ARG E 516 " --> pdb=" O ASP E 512 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP E 520 " --> pdb=" O ARG E 516 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU E 522 " --> pdb=" O LEU E 518 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN E 526 " --> pdb=" O GLU E 522 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN E 527 " --> pdb=" O LEU E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 559 Processing helix chain 'E' and resid 570 through 572 No H-bonds generated for 'chain 'E' and resid 570 through 572' Processing helix chain 'E' and resid 580 through 591 removed outlier: 4.127A pdb=" N ILE E 588 " --> pdb=" O ALA E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 608 No H-bonds generated for 'chain 'E' and resid 605 through 608' Processing helix chain 'E' and resid 620 through 623 No H-bonds generated for 'chain 'E' and resid 620 through 623' Processing helix chain 'E' and resid 649 through 654 Processing helix chain 'E' and resid 673 through 681 Processing helix chain 'E' and resid 688 through 698 Processing helix chain 'E' and resid 707 through 717 removed outlier: 3.550A pdb=" N ILE E 714 " --> pdb=" O LEU E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 732 Processing helix chain 'F' and resid 267 through 275 removed outlier: 3.824A pdb=" N GLN F 272 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY F 274 " --> pdb=" O ALA F 270 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS F 275 " --> pdb=" O ARG F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 291 No H-bonds generated for 'chain 'F' and resid 289 through 291' Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 330 through 333 No H-bonds generated for 'chain 'F' and resid 330 through 333' Processing helix chain 'F' and resid 346 through 349 Processing helix chain 'F' and resid 351 through 354 No H-bonds generated for 'chain 'F' and resid 351 through 354' Processing helix chain 'F' and resid 400 through 413 removed outlier: 3.837A pdb=" N ILE F 406 " --> pdb=" O GLY F 402 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG F 413 " --> pdb=" O ILE F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 430 Processing helix chain 'F' and resid 438 through 455 Processing helix chain 'F' and resid 499 through 502 No H-bonds generated for 'chain 'F' and resid 499 through 502' Processing helix chain 'F' and resid 512 through 529 removed outlier: 3.779A pdb=" N ASP F 520 " --> pdb=" O ARG F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 560 Processing helix chain 'F' and resid 570 through 572 No H-bonds generated for 'chain 'F' and resid 570 through 572' Processing helix chain 'F' and resid 578 through 591 removed outlier: 3.503A pdb=" N MET F 585 " --> pdb=" O LYS F 581 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE F 588 " --> pdb=" O ALA F 584 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 591 " --> pdb=" O LYS F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 608 No H-bonds generated for 'chain 'F' and resid 605 through 608' Processing helix chain 'F' and resid 620 through 627 Processing helix chain 'F' and resid 649 through 654 Processing helix chain 'F' and resid 673 through 681 Processing helix chain 'F' and resid 688 through 698 removed outlier: 3.708A pdb=" N VAL F 698 " --> pdb=" O ILE F 694 " (cutoff:3.500A) Processing helix chain 'F' and resid 707 through 718 Processing helix chain 'F' and resid 725 through 732 Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.307A pdb=" N ILE A 230 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 273 Processing helix chain 'A' and resid 288 through 291 removed outlier: 3.574A pdb=" N LEU A 291 " --> pdb=" O PRO A 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 288 through 291' Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.535A pdb=" N LEU A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 400 through 410 removed outlier: 3.529A pdb=" N ILE A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 426 through 429 No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 438 through 456 removed outlier: 3.730A pdb=" N GLY A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N MET A 453 " --> pdb=" O GLN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 501 No H-bonds generated for 'chain 'A' and resid 499 through 501' Processing helix chain 'A' and resid 512 through 530 removed outlier: 3.765A pdb=" N LEU A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP A 520 " --> pdb=" O ARG A 516 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.551A pdb=" N ALA A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 578 through 591 Processing helix chain 'A' and resid 605 through 608 No H-bonds generated for 'chain 'A' and resid 605 through 608' Processing helix chain 'A' and resid 620 through 629 removed outlier: 3.543A pdb=" N LEU A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 673 through 683 removed outlier: 3.640A pdb=" N LEU A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 698 removed outlier: 3.809A pdb=" N GLN A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 718 removed outlier: 3.642A pdb=" N LEU A 711 " --> pdb=" O ILE A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 733 Processing sheet with id= A, first strand: chain 'B' and resid 391 through 393 removed outlier: 3.899A pdb=" N VAL B 391 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B 369 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU B 258 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY B 371 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET B 372 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 663 through 667 removed outlier: 3.637A pdb=" N THR B 663 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU B 640 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N VAL B 539 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE B 642 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU B 541 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY B 644 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLY B 543 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR B 646 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 645 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE B 564 " --> pdb=" O CYS B 599 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL B 601 " --> pdb=" O PHE B 564 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS B 566 " --> pdb=" O VAL B 601 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 391 through 393 removed outlier: 4.075A pdb=" N VAL C 391 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL C 369 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU C 258 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY C 371 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS C 283 " --> pdb=" O ILE C 326 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 663 through 667 removed outlier: 3.721A pdb=" N THR C 663 " --> pdb=" O SER C 538 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU C 640 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL C 539 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE C 642 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU C 541 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY C 644 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N GLY C 543 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR C 646 " --> pdb=" O GLY C 543 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER C 598 " --> pdb=" O LEU C 641 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE C 643 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL C 600 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N THR C 645 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL C 602 " --> pdb=" O THR C 645 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE C 564 " --> pdb=" O CYS C 599 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL C 601 " --> pdb=" O PHE C 564 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LYS C 566 " --> pdb=" O VAL C 601 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 256 through 258 removed outlier: 6.285A pdb=" N VAL D 391 " --> pdb=" O LEU D 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 282 through 284 removed outlier: 6.808A pdb=" N ILE D 324 " --> pdb=" O LYS D 283 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 663 through 667 removed outlier: 3.789A pdb=" N THR D 663 " --> pdb=" O SER D 538 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU D 640 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL D 539 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE D 642 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU D 541 " --> pdb=" O ILE D 642 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLY D 644 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLY D 543 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR D 645 " --> pdb=" O VAL D 602 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE D 564 " --> pdb=" O CYS D 599 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL D 601 " --> pdb=" O PHE D 564 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS D 566 " --> pdb=" O VAL D 601 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 256 through 258 removed outlier: 6.256A pdb=" N VAL E 391 " --> pdb=" O LEU E 257 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'E' and resid 324 through 327 removed outlier: 5.929A pdb=" N LEU E 368 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N PHE E 327 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE E 370 " --> pdb=" O PHE E 327 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'E' and resid 663 through 667 removed outlier: 3.721A pdb=" N THR E 663 " --> pdb=" O SER E 538 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU E 640 " --> pdb=" O VAL E 537 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL E 539 " --> pdb=" O LEU E 640 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE E 642 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU E 541 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY E 644 " --> pdb=" O LEU E 541 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLY E 543 " --> pdb=" O GLY E 644 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 255 through 258 removed outlier: 5.571A pdb=" N VAL F 369 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU F 258 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY F 371 " --> pdb=" O LEU F 258 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 283 through 285 Processing sheet with id= M, first strand: chain 'F' and resid 663 through 665 removed outlier: 3.595A pdb=" N THR F 663 " --> pdb=" O SER F 538 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU F 640 " --> pdb=" O VAL F 537 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL F 539 " --> pdb=" O LEU F 640 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE F 642 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU F 541 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLY F 644 " --> pdb=" O LEU F 541 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE F 564 " --> pdb=" O CYS F 599 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL F 601 " --> pdb=" O PHE F 564 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS F 566 " --> pdb=" O VAL F 601 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 255 through 258 removed outlier: 5.780A pdb=" N VAL A 369 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU A 258 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY A 371 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 327 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A 372 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 283 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 663 through 666 removed outlier: 6.672A pdb=" N LEU A 640 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 539 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE A 642 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU A 541 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY A 644 " --> pdb=" O LEU A 541 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1533 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: 7.15 Time building geometry restraints manager: 11.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7206 1.33 - 1.45: 3428 1.45 - 1.57: 14098 1.57 - 1.69: 60 1.69 - 1.81: 240 Bond restraints: 25032 Sorted by residual: bond pdb=" C4 ATP F 801 " pdb=" C5 ATP F 801 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.79e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.62e+01 bond pdb=" C4 ATP F 802 " pdb=" C5 ATP F 802 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.44e+01 bond pdb=" C4 ATP E 801 " pdb=" C5 ATP E 801 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" C4 ATP E 802 " pdb=" C5 ATP E 802 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.16e+01 ... (remaining 25027 not shown) Histogram of bond angle deviations from ideal: 97.60 - 107.03: 981 107.03 - 116.47: 16486 116.47 - 125.91: 15953 125.91 - 135.34: 355 135.34 - 144.78: 23 Bond angle restraints: 33798 Sorted by residual: angle pdb=" PB ATP D 802 " pdb=" O3B ATP D 802 " pdb=" PG ATP D 802 " ideal model delta sigma weight residual 139.87 116.98 22.89 1.00e+00 1.00e+00 5.24e+02 angle pdb=" PB ATP F 802 " pdb=" O3B ATP F 802 " pdb=" PG ATP F 802 " ideal model delta sigma weight residual 139.87 117.75 22.12 1.00e+00 1.00e+00 4.89e+02 angle pdb=" PB ATP E 801 " pdb=" O3B ATP E 801 " pdb=" PG ATP E 801 " ideal model delta sigma weight residual 139.87 118.33 21.54 1.00e+00 1.00e+00 4.64e+02 angle pdb=" PB ATP C 802 " pdb=" O3B ATP C 802 " pdb=" PG ATP C 802 " ideal model delta sigma weight residual 139.87 118.51 21.36 1.00e+00 1.00e+00 4.56e+02 angle pdb=" PB ATP B 802 " pdb=" O3B ATP B 802 " pdb=" PG ATP B 802 " ideal model delta sigma weight residual 139.87 119.18 20.69 1.00e+00 1.00e+00 4.28e+02 ... (remaining 33793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.65: 14948 26.65 - 53.31: 383 53.31 - 79.96: 38 79.96 - 106.61: 2 106.61 - 133.27: 1 Dihedral angle restraints: 15372 sinusoidal: 6444 harmonic: 8928 Sorted by residual: dihedral pdb=" CA HIS B 417 " pdb=" C HIS B 417 " pdb=" N GLN B 418 " pdb=" CA GLN B 418 " ideal model delta harmonic sigma weight residual 180.00 46.73 133.27 0 5.00e+00 4.00e-02 7.10e+02 dihedral pdb=" CA GLY D 615 " pdb=" C GLY D 615 " pdb=" N PRO D 616 " pdb=" CA PRO D 616 " ideal model delta harmonic sigma weight residual 180.00 -130.37 -49.63 0 5.00e+00 4.00e-02 9.85e+01 dihedral pdb=" CA LYS D 462 " pdb=" C LYS D 462 " pdb=" N VAL D 463 " pdb=" CA VAL D 463 " ideal model delta harmonic sigma weight residual -180.00 -132.29 -47.71 0 5.00e+00 4.00e-02 9.11e+01 ... (remaining 15369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2940 0.067 - 0.133: 798 0.133 - 0.200: 113 0.200 - 0.267: 22 0.267 - 0.333: 3 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CB ILE C 302 " pdb=" CA ILE C 302 " pdb=" CG1 ILE C 302 " pdb=" CG2 ILE C 302 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CB THR B 494 " pdb=" CA THR B 494 " pdb=" OG1 THR B 494 " pdb=" CG2 THR B 494 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CG LEU D 473 " pdb=" CB LEU D 473 " pdb=" CD1 LEU D 473 " pdb=" CD2 LEU D 473 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 3873 not shown) Planarity restraints: 4308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 489 " 0.084 5.00e-02 4.00e+02 1.27e-01 2.58e+01 pdb=" N PRO B 490 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO B 490 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 490 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 287 " -0.062 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO C 288 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO C 288 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 288 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 287 " -0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO E 288 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO E 288 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 288 " -0.045 5.00e-02 4.00e+02 ... (remaining 4305 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4593 2.77 - 3.30: 23527 3.30 - 3.83: 39912 3.83 - 4.37: 48957 4.37 - 4.90: 78673 Nonbonded interactions: 195662 Sorted by model distance: nonbonded pdb=" OG SER A 421 " pdb=" OD1 ASP A 423 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR C 267 " pdb=" O3G ATP C 801 " model vdw 2.245 2.440 nonbonded pdb=" OE2 GLU D 468 " pdb=" OG SER D 472 " model vdw 2.278 2.440 nonbonded pdb=" O ARG C 232 " pdb=" OG SER D 450 " model vdw 2.281 2.440 nonbonded pdb=" OG SER F 569 " pdb=" OD1 ASP F 571 " model vdw 2.300 2.440 ... (remaining 195657 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 138 5.16 5 C 15486 2.51 5 N 4302 2.21 5 O 4698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 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: 0.020 Extract box with map and model: 3.250 Check model and map are aligned: 0.370 Process input model: 61.010 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.220 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 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 : 0.008 0.082 25032 Z= 0.505 Angle : 1.375 22.891 33798 Z= 0.890 Chirality : 0.061 0.333 3876 Planarity : 0.008 0.127 4308 Dihedral : 11.730 133.268 9600 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.19 % Favored : 87.68 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 1.11 % Twisted Proline : 3.03 % Twisted General : 0.77 % 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: -5.47 (0.11), residues: 3108 helix: -4.28 (0.07), residues: 1294 sheet: -2.35 (0.26), residues: 355 loop : -3.26 (0.14), residues: 1459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 861 time to evaluate : 3.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 867 average time/residue: 0.4350 time to fit residues: 555.1189 Evaluate side-chains 461 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 458 time to evaluate : 2.935 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2158 time to fit residues: 5.5383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 148 optimal weight: 0.3980 chunk 182 optimal weight: 6.9990 chunk 283 optimal weight: 9.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 HIS ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN B 365 ASN B 418 GLN B 505 ASN B 530 ASN B 546 HIS ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 GLN D 252 HIS ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 GLN ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 496 GLN E 505 ASN E 546 HIS E 561 ASN E 659 ASN F 417 HIS ** F 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 486 ASN F 526 GLN ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 HIS A 319 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN A 505 ASN A 653 GLN A 659 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 25032 Z= 0.271 Angle : 0.822 20.981 33798 Z= 0.417 Chirality : 0.048 0.262 3876 Planarity : 0.006 0.120 4308 Dihedral : 9.005 86.817 3360 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.59 % Favored : 89.29 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.11 % Twisted Proline : 2.27 % Twisted General : 0.44 % 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: -4.28 (0.13), residues: 3108 helix: -2.94 (0.11), residues: 1331 sheet: -1.90 (0.27), residues: 349 loop : -2.91 (0.15), residues: 1428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 517 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 44 residues processed: 575 average time/residue: 0.3710 time to fit residues: 334.7365 Evaluate side-chains 464 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 420 time to evaluate : 3.193 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.2330 time to fit residues: 23.6835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 235 optimal weight: 0.0370 chunk 192 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 283 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 252 optimal weight: 10.0000 chunk 281 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 227 optimal weight: 30.0000 overall best weight: 1.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 ASN D 405 GLN ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 HIS ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 496 GLN F 449 GLN ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 HIS A 301 ASN A 319 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 25032 Z= 0.205 Angle : 0.756 20.029 33798 Z= 0.380 Chirality : 0.046 0.284 3876 Planarity : 0.005 0.108 4308 Dihedral : 8.401 88.728 3360 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.55 % Favored : 89.38 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 1.11 % Twisted Proline : 1.52 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.14), residues: 3108 helix: -2.12 (0.13), residues: 1317 sheet: -1.70 (0.27), residues: 357 loop : -2.61 (0.16), residues: 1434 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 457 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 21 residues processed: 500 average time/residue: 0.3762 time to fit residues: 300.7023 Evaluate side-chains 413 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 392 time to evaluate : 3.374 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2584 time to fit residues: 14.0182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 5.9990 chunk 213 optimal weight: 20.0000 chunk 147 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 284 optimal weight: 5.9990 chunk 301 optimal weight: 0.0770 chunk 148 optimal weight: 5.9990 chunk 269 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 ASN B 449 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 GLN D 454 ASN D 496 GLN ** D 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 GLN ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 25032 Z= 0.279 Angle : 0.763 20.562 33798 Z= 0.383 Chirality : 0.047 0.293 3876 Planarity : 0.005 0.107 4308 Dihedral : 8.214 89.290 3360 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.39 % Favored : 88.55 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.14 % Twisted Proline : 3.03 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.14), residues: 3108 helix: -1.68 (0.13), residues: 1351 sheet: -1.63 (0.27), residues: 361 loop : -2.51 (0.16), residues: 1396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 425 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 43 residues processed: 470 average time/residue: 0.3567 time to fit residues: 269.5686 Evaluate side-chains 430 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 387 time to evaluate : 2.951 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2371 time to fit residues: 23.3389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 208 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 270 optimal weight: 0.0570 chunk 76 optimal weight: 0.7980 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 HIS ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN D 505 ASN ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 ASN ** F 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 25032 Z= 0.222 Angle : 0.727 21.683 33798 Z= 0.363 Chirality : 0.046 0.272 3876 Planarity : 0.005 0.107 4308 Dihedral : 7.947 88.549 3360 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.71 % Favored : 89.22 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.30 % Cis-general : 1.14 % Twisted Proline : 2.27 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.15), residues: 3108 helix: -1.24 (0.14), residues: 1340 sheet: -1.46 (0.27), residues: 368 loop : -2.41 (0.16), residues: 1400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 427 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 23 residues processed: 461 average time/residue: 0.3758 time to fit residues: 277.9760 Evaluate side-chains 401 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 378 time to evaluate : 2.998 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2316 time to fit residues: 14.2199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 0.0070 chunk 271 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 177 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 301 optimal weight: 4.9990 chunk 250 optimal weight: 9.9990 chunk 139 optimal weight: 0.0470 chunk 25 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 158 optimal weight: 0.0170 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN D 410 HIS ** D 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 435 ASN ** E 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 25032 Z= 0.153 Angle : 0.709 19.949 33798 Z= 0.350 Chirality : 0.045 0.285 3876 Planarity : 0.005 0.095 4308 Dihedral : 7.512 89.489 3360 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.10 % Favored : 89.83 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 1.14 % Twisted Proline : 0.76 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.15), residues: 3108 helix: -0.95 (0.14), residues: 1363 sheet: -1.20 (0.28), residues: 361 loop : -2.31 (0.16), residues: 1384 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 461 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 20 residues processed: 492 average time/residue: 0.3678 time to fit residues: 289.3486 Evaluate side-chains 408 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 388 time to evaluate : 2.937 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2271 time to fit residues: 12.6911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-dev-4877/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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-4877/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-4877/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-4877/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-4877/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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-4877/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-4877/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-4877/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-4877/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: 71.3242 > 50: distance: 48 - 53: 34.831 distance: 54 - 55: 40.883 distance: 54 - 57: 51.391 distance: 55 - 56: 50.339 distance: 57 - 58: 7.268 distance: 58 - 59: 39.585 distance: 59 - 60: 55.927 distance: 62 - 63: 17.989 distance: 63 - 64: 20.955 distance: 63 - 66: 22.143 distance: 66 - 67: 47.954 distance: 67 - 68: 34.058 distance: 67 - 69: 9.958 distance: 70 - 71: 41.232 distance: 71 - 72: 37.380 distance: 72 - 73: 41.086 distance: 72 - 78: 37.651 distance: 74 - 75: 8.552 distance: 75 - 76: 20.711 distance: 75 - 77: 8.779 distance: 78 - 79: 6.382 distance: 79 - 80: 52.787 distance: 79 - 82: 32.892 distance: 80 - 81: 39.200 distance: 80 - 86: 56.889 distance: 82 - 83: 41.180 distance: 82 - 84: 53.175 distance: 83 - 85: 56.851 distance: 86 - 87: 13.900 distance: 87 - 88: 14.478 distance: 87 - 90: 18.115 distance: 88 - 89: 38.856 distance: 88 - 95: 39.877 distance: 90 - 91: 32.092 distance: 93 - 94: 63.158 distance: 96 - 99: 3.730 distance: 97 - 98: 38.716 distance: 97 - 102: 38.827 distance: 99 - 100: 3.862 distance: 102 - 103: 3.992 distance: 103 - 104: 40.163 distance: 103 - 106: 5.777 distance: 104 - 105: 40.486 distance: 104 - 107: 40.657 distance: 107 - 108: 6.087 distance: 108 - 109: 37.738 distance: 108 - 111: 51.256 distance: 109 - 110: 17.164 distance: 109 - 118: 46.592 distance: 112 - 113: 3.059 distance: 112 - 114: 44.927 distance: 113 - 115: 34.586 distance: 114 - 116: 18.207 distance: 115 - 117: 49.551 distance: 116 - 117: 40.418 distance: 118 - 119: 55.709 distance: 119 - 120: 39.282 distance: 120 - 121: 39.267 distance: 120 - 122: 20.751 distance: 122 - 123: 7.848 distance: 123 - 124: 38.930 distance: 123 - 126: 39.302 distance: 124 - 125: 20.728 distance: 124 - 129: 15.143 distance: 126 - 127: 11.962 distance: 126 - 128: 46.550