Starting phenix.real_space_refine on Fri Mar 15 18:37:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuh_34107/03_2024/7yuh_34107.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuh_34107/03_2024/7yuh_34107.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/7yuh_34107/03_2024/7yuh_34107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuh_34107/03_2024/7yuh_34107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuh_34107/03_2024/7yuh_34107.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuh_34107/03_2024/7yuh_34107.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.056 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 7860 2.51 5 N 2178 2.21 5 O 2349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 519": "NH1" <-> "NH2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 312": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B ARG 479": "NH1" <-> "NH2" Residue "B ARG 503": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "B ARG 529": "NH1" <-> "NH2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "C ARG 250": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 345": "NH1" <-> "NH2" Residue "C ARG 366": "NH1" <-> "NH2" Residue "C ARG 370": "NH1" <-> "NH2" Residue "C ARG 479": "NH1" <-> "NH2" Residue "C ARG 503": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C ARG 519": "NH1" <-> "NH2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 694": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12432 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Chain: "B" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Chain: "C" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Time building chain proxies: 6.60, per 1000 atoms: 0.53 Number of scatterers: 12432 At special positions: 0 Unit cell: (97.58, 109.88, 138.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 2349 8.00 N 2178 7.00 C 7860 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: 4.32 Conformation dependent library (CDL) restraints added in 2.4 seconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 14 sheets defined 46.7% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 243 through 256 removed outlier: 3.899A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 280 through 294 removed outlier: 4.009A pdb=" N THR A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.736A pdb=" N ARG A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 372 Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 424 through 427 removed outlier: 3.774A pdb=" N MET A 427 " --> pdb=" O ILE A 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 424 through 427' Processing helix chain 'A' and resid 434 through 443 removed outlier: 4.164A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.569A pdb=" N ASP A 483 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 513 removed outlier: 3.999A pdb=" N LYS A 509 " --> pdb=" O TYR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.549A pdb=" N ILE A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.701A pdb=" N GLU A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 4.089A pdb=" N TYR A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 591 removed outlier: 4.309A pdb=" N GLU A 591 " --> pdb=" O ALA A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 645 Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.901A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 741 through 746 removed outlier: 3.727A pdb=" N LEU A 746 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 removed outlier: 3.595A pdb=" N LEU A 751 " --> pdb=" O PRO A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.603A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 254 Processing helix chain 'B' and resid 259 through 273 Processing helix chain 'B' and resid 281 through 296 removed outlier: 3.759A pdb=" N ALA B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.774A pdb=" N THR B 339 " --> pdb=" O VAL B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 373 Processing helix chain 'B' and resid 386 through 391 removed outlier: 3.857A pdb=" N ILE B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.808A pdb=" N HIS B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 444 Processing helix chain 'B' and resid 447 through 451 removed outlier: 3.673A pdb=" N PHE B 451 " --> pdb=" O ASN B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.677A pdb=" N ASP B 483 " --> pdb=" O ARG B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.664A pdb=" N TYR B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 removed outlier: 3.500A pdb=" N GLU B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 579 removed outlier: 3.998A pdb=" N TYR B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.997A pdb=" N GLU B 589 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 647 removed outlier: 3.861A pdb=" N LYS B 634 " --> pdb=" O GLY B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 652 removed outlier: 3.780A pdb=" N TYR B 651 " --> pdb=" O THR B 648 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 652 " --> pdb=" O GLN B 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 648 through 652' Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 728 removed outlier: 3.750A pdb=" N LYS B 721 " --> pdb=" O GLY B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 738 No H-bonds generated for 'chain 'B' and resid 736 through 738' Processing helix chain 'B' and resid 739 through 744 removed outlier: 3.764A pdb=" N GLU B 744 " --> pdb=" O GLU B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 769 removed outlier: 3.759A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 282 through 294 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.631A pdb=" N THR C 311 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 339 Processing helix chain 'C' and resid 360 through 372 Processing helix chain 'C' and resid 386 through 391 removed outlier: 3.647A pdb=" N ILE C 390 " --> pdb=" O ASP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 411 Processing helix chain 'C' and resid 434 through 444 removed outlier: 4.158A pdb=" N ALA C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET C 439 " --> pdb=" O PRO C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 451 removed outlier: 3.500A pdb=" N THR C 450 " --> pdb=" O GLN C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.784A pdb=" N ASP C 483 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 505 through 513 removed outlier: 3.651A pdb=" N LYS C 509 " --> pdb=" O TYR C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 533 removed outlier: 3.798A pdb=" N ILE C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 removed outlier: 3.795A pdb=" N GLU C 560 " --> pdb=" O LYS C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 579 Processing helix chain 'C' and resid 630 through 647 removed outlier: 4.096A pdb=" N LYS C 634 " --> pdb=" O GLY C 630 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 652 removed outlier: 4.199A pdb=" N TYR C 651 " --> pdb=" O THR C 648 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY C 652 " --> pdb=" O GLN C 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 648 through 652' Processing helix chain 'C' and resid 679 through 693 Processing helix chain 'C' and resid 717 through 728 removed outlier: 3.642A pdb=" N LYS C 721 " --> pdb=" O GLY C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 745 removed outlier: 4.349A pdb=" N ALA C 741 " --> pdb=" O ASP C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 removed outlier: 4.275A pdb=" N LEU C 751 " --> pdb=" O PRO C 747 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU C 752 " --> pdb=" O LYS C 748 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY C 753 " --> pdb=" O GLU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 769 Processing sheet with id=AA1, first strand: chain 'A' and resid 375 through 380 removed outlier: 6.824A pdb=" N LYS A 375 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 420 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N HIS A 377 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ASP A 422 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 379 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 468 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ILE A 419 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N THR A 470 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU A 421 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU A 353 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 488 " --> pdb=" O VAL A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 7.208A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 597 through 603 removed outlier: 6.668A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.008A pdb=" N ILE A 733 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL A 759 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU A 735 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 352 through 354 removed outlier: 6.132A pdb=" N VAL B 352 " --> pdb=" O ILE B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 376 through 380 Processing sheet with id=AA7, first strand: chain 'B' and resid 596 through 603 removed outlier: 3.541A pdb=" N THR B 603 " --> pdb=" O GLY B 606 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 700 through 702 Processing sheet with id=AA9, first strand: chain 'B' and resid 705 through 707 removed outlier: 4.121A pdb=" N GLU B 705 " --> pdb=" O MET B 713 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS B 711 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 376 through 380 removed outlier: 3.804A pdb=" N LEU C 420 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU C 353 " --> pdb=" O ALA C 471 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL C 352 " --> pdb=" O ILE C 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 520 through 522 removed outlier: 5.967A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 596 through 603 removed outlier: 5.988A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.758A pdb=" N ALA C 701 " --> pdb=" O VAL C 734 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE C 733 " --> pdb=" O LYS C 757 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL C 759 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU C 735 " --> pdb=" O VAL C 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 705 through 707 removed outlier: 4.050A pdb=" N GLU C 705 " --> pdb=" O MET C 713 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS C 711 " --> pdb=" O SER C 707 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1380 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: 3.40 Time building geometry restraints manager: 4.80 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: 3592 1.33 - 1.45: 1928 1.45 - 1.57: 7053 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 12663 Sorted by residual: bond pdb=" C ARG C 479 " pdb=" N PRO C 480 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.20e-02 6.94e+03 1.27e+01 bond pdb=" C LEU C 771 " pdb=" N PRO C 772 " ideal model delta sigma weight residual 1.333 1.370 -0.037 1.20e-02 6.94e+03 9.42e+00 bond pdb=" C LEU C 381 " pdb=" N GLY C 382 " ideal model delta sigma weight residual 1.331 1.312 0.019 6.60e-03 2.30e+04 8.38e+00 bond pdb=" C LEU B 351 " pdb=" N VAL B 352 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.24e-02 6.50e+03 6.06e+00 bond pdb=" C GLY C 321 " pdb=" N LEU C 322 " ideal model delta sigma weight residual 1.333 1.300 0.032 1.38e-02 5.25e+03 5.54e+00 ... (remaining 12658 not shown) Histogram of bond angle deviations from ideal: 97.43 - 105.01: 342 105.01 - 112.59: 6606 112.59 - 120.16: 5239 120.16 - 127.74: 4846 127.74 - 135.32: 130 Bond angle restraints: 17163 Sorted by residual: angle pdb=" N GLY B 341 " pdb=" CA GLY B 341 " pdb=" C GLY B 341 " ideal model delta sigma weight residual 115.00 107.27 7.73 1.44e+00 4.82e-01 2.88e+01 angle pdb=" C GLY B 321 " pdb=" N LEU B 322 " pdb=" CA LEU B 322 " ideal model delta sigma weight residual 121.54 131.18 -9.64 1.91e+00 2.74e-01 2.55e+01 angle pdb=" N PRO A 592 " pdb=" CA PRO A 592 " pdb=" C PRO A 592 " ideal model delta sigma weight residual 112.47 122.78 -10.31 2.06e+00 2.36e-01 2.50e+01 angle pdb=" N PRO B 281 " pdb=" CA PRO B 281 " pdb=" C PRO B 281 " ideal model delta sigma weight residual 112.47 121.60 -9.13 2.06e+00 2.36e-01 1.97e+01 angle pdb=" C GLU A 591 " pdb=" N PRO A 592 " pdb=" CA PRO A 592 " ideal model delta sigma weight residual 119.84 125.07 -5.23 1.25e+00 6.40e-01 1.75e+01 ... (remaining 17158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 7280 15.45 - 30.90: 407 30.90 - 46.36: 83 46.36 - 61.81: 7 61.81 - 77.26: 14 Dihedral angle restraints: 7791 sinusoidal: 3225 harmonic: 4566 Sorted by residual: dihedral pdb=" CA SER B 280 " pdb=" C SER B 280 " pdb=" N PRO B 281 " pdb=" CA PRO B 281 " ideal model delta harmonic sigma weight residual 180.00 -140.53 -39.47 0 5.00e+00 4.00e-02 6.23e+01 dihedral pdb=" CA LEU C 306 " pdb=" C LEU C 306 " pdb=" N ASP C 307 " pdb=" CA ASP C 307 " ideal model delta harmonic sigma weight residual -180.00 -140.66 -39.34 0 5.00e+00 4.00e-02 6.19e+01 dihedral pdb=" CA GLY B 279 " pdb=" C GLY B 279 " pdb=" N SER B 280 " pdb=" CA SER B 280 " ideal model delta harmonic sigma weight residual 180.00 145.73 34.27 0 5.00e+00 4.00e-02 4.70e+01 ... (remaining 7788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1306 0.062 - 0.124: 547 0.124 - 0.185: 81 0.185 - 0.247: 12 0.247 - 0.309: 7 Chirality restraints: 1953 Sorted by residual: chirality pdb=" CB ILE B 468 " pdb=" CA ILE B 468 " pdb=" CG1 ILE B 468 " pdb=" CG2 ILE B 468 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB ILE B 398 " pdb=" CA ILE B 398 " pdb=" CG1 ILE B 398 " pdb=" CG2 ILE B 398 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1950 not shown) Planarity restraints: 2229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 771 " 0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO C 772 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 772 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 772 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 507 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO B 508 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 508 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 508 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 507 " -0.045 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO A 508 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 508 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 508 " -0.038 5.00e-02 4.00e+02 ... (remaining 2226 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2707 2.78 - 3.31: 11149 3.31 - 3.84: 19725 3.84 - 4.37: 22730 4.37 - 4.90: 38493 Nonbonded interactions: 94804 Sorted by model distance: nonbonded pdb=" O PRO A 297 " pdb=" OH TYR A 460 " model vdw 2.253 2.440 nonbonded pdb=" OG1 THR A 672 " pdb=" O LYS A 674 " model vdw 2.282 2.440 nonbonded pdb=" OD1 ASP A 422 " pdb=" OG1 THR A 470 " model vdw 2.284 2.440 nonbonded pdb=" OG1 THR B 603 " pdb=" O GLY B 606 " model vdw 2.286 2.440 nonbonded pdb=" O PRO B 297 " pdb=" OH TYR B 460 " model vdw 2.286 2.440 ... (remaining 94799 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' } 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=0.00 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: 1.900 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: 8.550 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 34.140 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 : 0.010 0.089 12663 Z= 0.634 Angle : 1.176 12.505 17163 Z= 0.628 Chirality : 0.065 0.309 1953 Planarity : 0.009 0.081 2229 Dihedral : 10.784 77.262 4863 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.94 % Favored : 88.93 % Rotamer: Outliers : 0.15 % Allowed : 3.84 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -4.68 (0.16), residues: 1590 helix: -2.80 (0.15), residues: 638 sheet: -2.89 (0.31), residues: 195 loop : -3.43 (0.18), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP B 558 HIS 0.020 0.003 HIS C 319 PHE 0.029 0.004 PHE C 466 TYR 0.032 0.003 TYR A 289 ARG 0.019 0.002 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 321 time to evaluate : 1.355 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: A 276 MET cc_start: 0.6217 (mtt) cc_final: 0.5102 (tpp) REVERT: A 439 MET cc_start: 0.8421 (mmm) cc_final: 0.8210 (mmm) REVERT: A 453 ASP cc_start: 0.6704 (m-30) cc_final: 0.6322 (m-30) REVERT: A 454 HIS cc_start: 0.7609 (m90) cc_final: 0.7404 (m-70) REVERT: A 469 THR cc_start: 0.9165 (m) cc_final: 0.8840 (p) REVERT: A 516 MET cc_start: 0.8151 (mmm) cc_final: 0.7565 (mtm) REVERT: A 520 ILE cc_start: 0.8595 (mt) cc_final: 0.8349 (mm) REVERT: A 553 LYS cc_start: 0.8785 (mmmm) cc_final: 0.8465 (mmmt) REVERT: A 608 THR cc_start: 0.8551 (t) cc_final: 0.8130 (p) REVERT: A 641 LEU cc_start: 0.8396 (mt) cc_final: 0.8132 (mm) REVERT: B 292 TRP cc_start: 0.7638 (m100) cc_final: 0.7362 (m100) REVERT: B 385 ARG cc_start: 0.7692 (pmt170) cc_final: 0.7191 (mtm-85) REVERT: B 439 MET cc_start: 0.7732 (mmp) cc_final: 0.7484 (mmp) REVERT: C 244 SER cc_start: 0.8386 (p) cc_final: 0.8088 (t) REVERT: C 290 LEU cc_start: 0.8822 (mt) cc_final: 0.8312 (pp) REVERT: C 721 LYS cc_start: 0.8397 (mttm) cc_final: 0.8156 (mtpp) outliers start: 2 outliers final: 1 residues processed: 323 average time/residue: 0.3299 time to fit residues: 139.7610 Evaluate side-chains 164 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 590 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 1.9990 chunk 120 optimal weight: 0.0570 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 144 optimal weight: 9.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 310 HIS A 319 HIS A 346 ASN A 411 GLN A 739 ASN B 346 ASN B 449 ASN B 664 HIS C 346 ASN C 393 HIS C 407 HIS C 449 ASN C 454 HIS C 472 ASN C 598 GLN C 647 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12663 Z= 0.194 Angle : 0.709 8.823 17163 Z= 0.357 Chirality : 0.045 0.186 1953 Planarity : 0.006 0.063 2229 Dihedral : 6.431 32.978 1744 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.63 % Allowed : 10.68 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.01 (0.19), residues: 1590 helix: -0.99 (0.19), residues: 665 sheet: -2.22 (0.36), residues: 179 loop : -2.92 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 558 HIS 0.010 0.001 HIS A 310 PHE 0.009 0.001 PHE A 451 TYR 0.022 0.002 TYR A 289 ARG 0.010 0.001 ARG B 552 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 224 time to evaluate : 1.534 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: A 276 MET cc_start: 0.6228 (mtt) cc_final: 0.5140 (tpp) REVERT: A 469 THR cc_start: 0.8992 (m) cc_final: 0.8604 (p) REVERT: A 516 MET cc_start: 0.7977 (mmm) cc_final: 0.7518 (mtm) REVERT: A 520 ILE cc_start: 0.8530 (mt) cc_final: 0.8161 (mm) REVERT: A 553 LYS cc_start: 0.8570 (mmmm) cc_final: 0.8299 (mmmt) REVERT: A 608 THR cc_start: 0.8414 (t) cc_final: 0.7931 (p) REVERT: A 620 SER cc_start: 0.9013 (p) cc_final: 0.8789 (t) REVERT: A 631 GLU cc_start: 0.7723 (tp30) cc_final: 0.6484 (tp30) REVERT: B 385 ARG cc_start: 0.7739 (pmt170) cc_final: 0.7200 (mtm-85) REVERT: B 552 ARG cc_start: 0.7905 (mtt-85) cc_final: 0.7505 (mtt-85) REVERT: B 567 ARG cc_start: 0.7377 (mmt-90) cc_final: 0.7134 (mmt-90) REVERT: B 681 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.7901 (mm) REVERT: B 750 VAL cc_start: 0.8527 (t) cc_final: 0.8202 (t) REVERT: C 268 LYS cc_start: 0.8352 (ttpp) cc_final: 0.8003 (tppt) outliers start: 35 outliers final: 13 residues processed: 245 average time/residue: 0.2989 time to fit residues: 100.1536 Evaluate side-chains 173 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 159 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 723 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 0.0370 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 98 optimal weight: 0.0170 chunk 39 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS A 346 ASN B 454 HIS B 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12663 Z= 0.210 Angle : 0.680 10.638 17163 Z= 0.338 Chirality : 0.045 0.188 1953 Planarity : 0.006 0.061 2229 Dihedral : 5.910 29.665 1744 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.54 % Allowed : 12.42 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.20), residues: 1590 helix: -0.39 (0.20), residues: 675 sheet: -1.95 (0.35), residues: 203 loop : -2.89 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 292 HIS 0.008 0.001 HIS A 310 PHE 0.008 0.001 PHE C 466 TYR 0.020 0.002 TYR B 768 ARG 0.006 0.001 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 179 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6219 (mtt) cc_final: 0.5110 (tpp) REVERT: A 401 MET cc_start: 0.5437 (tmm) cc_final: 0.5188 (tmm) REVERT: A 423 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7539 (tt0) REVERT: A 469 THR cc_start: 0.9059 (m) cc_final: 0.8651 (p) REVERT: A 516 MET cc_start: 0.7987 (mmm) cc_final: 0.7492 (mtm) REVERT: A 520 ILE cc_start: 0.8571 (mt) cc_final: 0.8211 (mm) REVERT: A 553 LYS cc_start: 0.8613 (mmmm) cc_final: 0.8349 (mmmt) REVERT: A 608 THR cc_start: 0.8489 (t) cc_final: 0.7990 (p) REVERT: A 620 SER cc_start: 0.8984 (p) cc_final: 0.8756 (t) REVERT: A 735 LEU cc_start: 0.8121 (tp) cc_final: 0.7905 (tp) REVERT: B 385 ARG cc_start: 0.7825 (pmt170) cc_final: 0.7237 (mtm-85) REVERT: B 546 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: B 552 ARG cc_start: 0.7982 (mtt-85) cc_final: 0.7579 (mtt-85) REVERT: B 584 ARG cc_start: 0.7240 (ttt-90) cc_final: 0.6648 (ttt-90) outliers start: 47 outliers final: 28 residues processed: 211 average time/residue: 0.2726 time to fit residues: 80.4746 Evaluate side-chains 185 residues out of total 1329 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 437 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 698 MET Chi-restraints excluded: chain B residue 726 HIS Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 708 LEU Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 746 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 62.074 > 50: distance: 19 - 95: 19.385 distance: 22 - 92: 18.499 distance: 29 - 80: 22.395 distance: 31 - 34: 26.697 distance: 32 - 77: 23.039 distance: 34 - 35: 5.813 distance: 35 - 36: 20.399 distance: 35 - 38: 10.292 distance: 36 - 37: 44.403 distance: 36 - 48: 14.272 distance: 38 - 39: 7.678 distance: 39 - 40: 7.940 distance: 39 - 41: 6.411 distance: 40 - 42: 8.190 distance: 41 - 43: 5.469 distance: 41 - 44: 4.869 distance: 42 - 43: 5.312 distance: 43 - 45: 7.814 distance: 44 - 46: 11.579 distance: 46 - 47: 3.066 distance: 48 - 49: 12.994 distance: 48 - 72: 23.657 distance: 49 - 50: 10.822 distance: 49 - 52: 38.734 distance: 50 - 51: 14.420 distance: 50 - 55: 28.828 distance: 51 - 69: 5.075 distance: 52 - 53: 62.074 distance: 52 - 54: 51.815 distance: 55 - 56: 6.648 distance: 55 - 61: 9.140 distance: 56 - 57: 18.205 distance: 56 - 59: 14.993 distance: 57 - 58: 12.436 distance: 57 - 62: 6.308 distance: 59 - 60: 4.572 distance: 60 - 61: 10.209 distance: 62 - 63: 25.502 distance: 63 - 64: 21.608 distance: 63 - 66: 19.610 distance: 64 - 65: 7.562 distance: 64 - 69: 9.495 distance: 66 - 67: 26.869 distance: 66 - 68: 17.622 distance: 69 - 70: 39.495 distance: 70 - 71: 16.880 distance: 71 - 72: 20.480 distance: 71 - 73: 10.061 distance: 73 - 74: 19.569 distance: 74 - 75: 7.831 distance: 75 - 76: 40.159 distance: 75 - 77: 33.882 distance: 77 - 78: 17.949 distance: 78 - 79: 12.801 distance: 78 - 81: 7.464 distance: 79 - 80: 12.409 distance: 79 - 84: 9.894 distance: 81 - 82: 19.889 distance: 81 - 83: 36.173 distance: 84 - 85: 31.219 distance: 85 - 86: 10.505 distance: 85 - 88: 14.901 distance: 86 - 87: 3.371 distance: 86 - 92: 18.172 distance: 88 - 89: 13.235 distance: 89 - 90: 11.832 distance: 89 - 91: 16.391 distance: 92 - 93: 19.577 distance: 93 - 94: 11.087 distance: 93 - 96: 9.312 distance: 94 - 95: 24.844 distance: 94 - 100: 14.008 distance: 96 - 97: 7.422 distance: 97 - 98: 12.602 distance: 97 - 99: 9.666 distance: 100 - 101: 21.053 distance: 101 - 102: 14.413 distance: 101 - 104: 25.458 distance: 102 - 103: 21.973 distance: 102 - 107: 15.272 distance: 104 - 105: 18.251 distance: 104 - 106: 5.222