Starting phenix.real_space_refine on Mon Dec 11 03:45:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yum_34108/12_2023/7yum_34108.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yum_34108/12_2023/7yum_34108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yum_34108/12_2023/7yum_34108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yum_34108/12_2023/7yum_34108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yum_34108/12_2023/7yum_34108.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yum_34108/12_2023/7yum_34108.pdb" } resolution = 3.8 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= 0.055 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 60 5.16 5 C 10480 2.51 5 N 2904 2.21 5 O 3132 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 ARG 567": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A PHE 657": "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 PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 567": "NH1" <-> "NH2" Residue "B TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 567": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "D ARG 366": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "D ARG 479": "NH1" <-> "NH2" Residue "D TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 503": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D ARG 519": "NH1" <-> "NH2" Residue "D ARG 529": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 694": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 16576 Number of models: 1 Model: "" Number of chains: 4 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} Chain: "D" 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: 8.72, per 1000 atoms: 0.53 Number of scatterers: 16576 At special positions: 0 Unit cell: (118.08, 109.88, 143.5, 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 60 16.00 O 3132 8.00 N 2904 7.00 C 10480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.04 Conformation dependent library (CDL) restraints added in 3.1 seconds 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3904 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 18 sheets defined 44.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 245 through 255 removed outlier: 4.145A pdb=" N LYS A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 removed outlier: 4.254A pdb=" N ARG A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.770A pdb=" N VAL A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 403 through 411 removed outlier: 3.756A pdb=" N HIS A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 444 removed outlier: 3.529A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.566A pdb=" N THR A 450 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 447 through 451' Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.672A pdb=" N LYS A 509 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.670A pdb=" N GLU A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.733A pdb=" N TYR A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 647 Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.980A 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 761 through 770 removed outlier: 3.792A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 283 through 296 removed outlier: 3.847A pdb=" N VAL B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 325 through 339 removed outlier: 4.034A pdb=" N ILE B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 373 removed outlier: 3.660A pdb=" N ASN B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 403 through 412 removed outlier: 3.678A pdb=" N VAL B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 444 removed outlier: 4.122A pdb=" N ALA B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 removed outlier: 3.721A pdb=" N THR B 450 " --> pdb=" O GLN B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 506 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.636A pdb=" N ILE B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 573 through 579 removed outlier: 3.651A pdb=" N TYR B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 647 removed outlier: 3.771A pdb=" N LYS B 634 " --> pdb=" O GLY B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 652 removed outlier: 3.749A pdb=" N GLY B 652 " --> pdb=" O GLN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 728 removed outlier: 4.100A pdb=" N LYS B 721 " --> pdb=" O GLY B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 740 No H-bonds generated for 'chain 'B' and resid 738 through 740' Processing helix chain 'B' and resid 742 through 746 Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.715A pdb=" N LEU B 751 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 769 removed outlier: 3.714A 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 269 Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.558A pdb=" N ARG C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 338 " --> pdb=" O ALA C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 372 Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 423 through 427 removed outlier: 4.073A pdb=" N MET C 427 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 444 removed outlier: 3.958A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.548A pdb=" N LEU C 482 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 515 removed outlier: 3.549A pdb=" N TYR C 505 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TRP C 507 " --> pdb=" O ARG C 503 " (cutoff:3.500A) Proline residue: C 508 - end of helix Processing helix chain 'C' and resid 523 through 534 removed outlier: 3.662A pdb=" N ILE C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 removed outlier: 3.514A pdb=" N GLU C 560 " --> pdb=" O LYS C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 579 removed outlier: 3.662A pdb=" N TYR C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 647 removed outlier: 3.652A pdb=" N LYS C 634 " --> pdb=" O GLY C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 693 Processing helix chain 'C' and resid 717 through 728 Processing helix chain 'C' and resid 747 through 752 Processing helix chain 'C' and resid 761 through 770 removed outlier: 3.526A pdb=" N VAL C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 255 removed outlier: 3.832A pdb=" N LYS D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 273 Processing helix chain 'D' and resid 283 through 296 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 324 through 337 removed outlier: 4.206A pdb=" N ARG D 328 " --> pdb=" O ASP D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 372 Processing helix chain 'D' and resid 386 through 390 removed outlier: 3.639A pdb=" N ILE D 390 " --> pdb=" O GLU D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 435 through 444 removed outlier: 3.822A pdb=" N MET D 439 " --> pdb=" O PRO D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 477 removed outlier: 3.711A pdb=" N THR D 476 " --> pdb=" O THR D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 514 removed outlier: 3.740A pdb=" N LYS D 509 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 512 " --> pdb=" O PRO D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.914A pdb=" N ILE D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 560 removed outlier: 3.527A pdb=" N GLU D 560 " --> pdb=" O LYS D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 630 through 647 removed outlier: 3.965A pdb=" N LYS D 634 " --> pdb=" O GLY D 630 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 636 " --> pdb=" O VAL D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 652 Processing helix chain 'D' and resid 679 through 691 Processing helix chain 'D' and resid 717 through 729 Processing helix chain 'D' and resid 738 through 745 removed outlier: 4.216A pdb=" N ALA D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 754 removed outlier: 3.912A pdb=" N LEU D 751 " --> pdb=" O PRO D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 769 Processing sheet with id=AA1, first strand: chain 'A' and resid 352 through 354 removed outlier: 6.014A pdb=" N VAL A 352 " --> pdb=" O ILE A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 418 through 422 removed outlier: 3.504A pdb=" N ILE A 468 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.405A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 596 through 603 removed outlier: 6.736A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 700 through 702 removed outlier: 6.751A pdb=" N ILE A 733 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL A 759 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 735 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 378 through 380 removed outlier: 6.384A pdb=" N ILE B 379 " --> pdb=" O ASP B 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 596 through 603 removed outlier: 3.703A pdb=" N THR B 603 " --> pdb=" O GLY B 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 732 through 736 removed outlier: 6.744A pdb=" N ILE B 733 " --> pdb=" O LYS B 757 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL B 759 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU B 735 " --> pdb=" O VAL B 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AB1, first strand: chain 'C' and resid 418 through 421 removed outlier: 3.604A pdb=" N ILE C 468 " --> pdb=" O ILE C 419 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 521 through 522 removed outlier: 6.302A 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 601 removed outlier: 6.186A 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: 6.986A pdb=" N ALA C 701 " --> pdb=" O VAL C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AB6, first strand: chain 'D' and resid 376 through 380 removed outlier: 6.227A pdb=" N HIS D 377 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP D 422 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE D 379 " --> pdb=" O ASP D 422 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 596 through 603 removed outlier: 5.537A pdb=" N LYS D 622 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL D 665 " --> pdb=" O LYS D 622 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 700 through 702 removed outlier: 6.426A pdb=" N ALA D 701 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE D 733 " --> pdb=" O LYS D 757 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL D 759 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU D 735 " --> pdb=" O VAL D 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 705 through 707 removed outlier: 3.759A pdb=" N GLU D 705 " --> pdb=" O MET D 713 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 6.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5284 1.34 - 1.45: 2577 1.45 - 1.57: 8903 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 16884 Sorted by residual: bond pdb=" C ILE B 419 " pdb=" N LEU B 420 " ideal model delta sigma weight residual 1.331 1.295 0.036 1.40e-02 5.10e+03 6.73e+00 bond pdb=" CG LEU B 769 " pdb=" CD1 LEU B 769 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.52e+00 bond pdb=" CG LEU B 723 " pdb=" CD1 LEU B 723 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.43e+00 bond pdb=" CB GLN C 499 " pdb=" CG GLN C 499 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.20e+00 bond pdb=" CG1 ILE B 468 " pdb=" CD1 ILE B 468 " ideal model delta sigma weight residual 1.513 1.420 0.093 3.90e-02 6.57e+02 5.69e+00 ... (remaining 16879 not shown) Histogram of bond angle deviations from ideal: 96.78 - 105.13: 459 105.13 - 113.47: 9652 113.47 - 121.82: 9082 121.82 - 130.16: 3581 130.16 - 138.51: 110 Bond angle restraints: 22884 Sorted by residual: angle pdb=" N GLY B 539 " pdb=" CA GLY B 539 " pdb=" C GLY B 539 " ideal model delta sigma weight residual 111.21 118.38 -7.17 1.04e+00 9.25e-01 4.76e+01 angle pdb=" C ALA D 400 " pdb=" N MET D 401 " pdb=" CA MET D 401 " ideal model delta sigma weight residual 120.97 138.51 -17.54 2.84e+00 1.24e-01 3.81e+01 angle pdb=" C GLY B 321 " pdb=" N LEU B 322 " pdb=" CA LEU B 322 " ideal model delta sigma weight residual 121.54 131.70 -10.16 1.91e+00 2.74e-01 2.83e+01 angle pdb=" C MET A 698 " pdb=" N ASP A 699 " pdb=" CA ASP A 699 " ideal model delta sigma weight residual 122.08 129.85 -7.77 1.47e+00 4.63e-01 2.80e+01 angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 109.34 99.73 9.61 2.08e+00 2.31e-01 2.13e+01 ... (remaining 22879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.15: 9612 15.15 - 30.31: 627 30.31 - 45.46: 120 45.46 - 60.62: 9 60.62 - 75.77: 20 Dihedral angle restraints: 10388 sinusoidal: 4300 harmonic: 6088 Sorted by residual: dihedral pdb=" CA GLU D 591 " pdb=" C GLU D 591 " pdb=" N PRO D 592 " pdb=" CA PRO D 592 " ideal model delta harmonic sigma weight residual 180.00 -132.24 -47.76 0 5.00e+00 4.00e-02 9.12e+01 dihedral pdb=" CA PRO B 673 " pdb=" C PRO B 673 " pdb=" N LYS B 674 " pdb=" CA LYS B 674 " ideal model delta harmonic sigma weight residual -180.00 -138.02 -41.98 0 5.00e+00 4.00e-02 7.05e+01 dihedral pdb=" CA LYS B 347 " pdb=" C LYS B 347 " pdb=" N ALA B 348 " pdb=" CA ALA B 348 " ideal model delta harmonic sigma weight residual 180.00 140.73 39.27 0 5.00e+00 4.00e-02 6.17e+01 ... (remaining 10385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2058 0.080 - 0.160: 485 0.160 - 0.240: 52 0.240 - 0.320: 6 0.320 - 0.400: 3 Chirality restraints: 2604 Sorted by residual: chirality pdb=" CB ILE C 379 " pdb=" CA ILE C 379 " pdb=" CG1 ILE C 379 " pdb=" CG2 ILE C 379 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.00e+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 2.28 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CG LEU C 462 " pdb=" CB LEU C 462 " pdb=" CD1 LEU C 462 " pdb=" CD2 LEU C 462 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 2601 not shown) Planarity restraints: 2972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 434 " -0.051 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO D 435 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 435 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 435 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 773 " 0.049 5.00e-02 4.00e+02 7.38e-02 8.70e+00 pdb=" N PRO A 774 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 774 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 774 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 356 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO C 357 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 357 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 357 " -0.037 5.00e-02 4.00e+02 ... (remaining 2969 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2181 2.75 - 3.29: 16004 3.29 - 3.82: 27292 3.82 - 4.36: 31640 4.36 - 4.90: 53127 Nonbonded interactions: 130244 Sorted by model distance: nonbonded pdb=" O LYS C 587 " pdb=" OG1 THR C 590 " model vdw 2.209 2.440 nonbonded pdb=" OG1 THR D 603 " pdb=" O GLY D 606 " model vdw 2.257 2.440 nonbonded pdb=" OG1 THR A 603 " pdb=" O GLY A 606 " model vdw 2.257 2.440 nonbonded pdb=" OD2 ASP A 425 " pdb=" OG1 THR A 473 " model vdw 2.259 2.440 nonbonded pdb=" O ARG C 336 " pdb=" OG1 THR C 339 " model vdw 2.260 2.440 ... (remaining 130239 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' } 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: 1.910 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: 8.850 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 42.920 Find NCS groups from input model: 0.960 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 0.110 16884 Z= 0.660 Angle : 1.257 17.540 22884 Z= 0.676 Chirality : 0.067 0.400 2604 Planarity : 0.009 0.077 2972 Dihedral : 11.165 75.772 6484 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.31 % Favored : 87.59 % Rotamer: Outliers : 0.34 % Allowed : 3.61 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.34 % Twisted General : 0.45 % 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: -4.61 (0.15), residues: 2120 helix: -2.79 (0.13), residues: 855 sheet: -2.52 (0.30), residues: 229 loop : -3.45 (0.16), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP D 563 HIS 0.020 0.003 HIS B 319 PHE 0.025 0.004 PHE A 467 TYR 0.039 0.004 TYR D 289 ARG 0.020 0.001 ARG D 374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 405 time to evaluate : 2.083 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 outliers start: 6 outliers final: 3 residues processed: 410 average time/residue: 0.3888 time to fit residues: 220.1848 Evaluate side-chains 231 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 228 time to evaluate : 2.020 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1544 time to fit residues: 3.6394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 192 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 ASN A 472 ASN A 475 GLN A 495 ASN A 598 GLN A 664 HIS B 377 HIS B 449 ASN B 475 GLN B 510 GLN B 726 HIS C 472 ASN C 726 HIS ** D 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 GLN D 628 GLN D 726 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16884 Z= 0.229 Angle : 0.781 12.189 22884 Z= 0.397 Chirality : 0.047 0.268 2604 Planarity : 0.006 0.066 2972 Dihedral : 7.112 46.891 2324 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 2.26 % Allowed : 11.63 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.05 % 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: -3.29 (0.16), residues: 2120 helix: -1.34 (0.16), residues: 863 sheet: -1.91 (0.32), residues: 213 loop : -3.04 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 563 HIS 0.006 0.001 HIS B 319 PHE 0.014 0.002 PHE A 466 TYR 0.021 0.002 TYR B 768 ARG 0.006 0.001 ARG B 391 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 284 time to evaluate : 1.950 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 outliers start: 40 outliers final: 21 residues processed: 307 average time/residue: 0.3408 time to fit residues: 149.3298 Evaluate side-chains 221 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 200 time to evaluate : 2.005 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1594 time to fit residues: 8.5551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 30.0000 chunk 59 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 chunk 131 optimal weight: 4.9990 chunk 53 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 346 ASN ** D 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 659 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16884 Z= 0.306 Angle : 0.789 10.205 22884 Z= 0.399 Chirality : 0.047 0.234 2604 Planarity : 0.006 0.065 2972 Dihedral : 6.816 43.997 2324 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 2.37 % Allowed : 14.79 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.10 % 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: -2.86 (0.17), residues: 2120 helix: -0.88 (0.17), residues: 863 sheet: -1.75 (0.31), residues: 231 loop : -2.89 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 298 HIS 0.010 0.001 HIS B 319 PHE 0.059 0.003 PHE D 557 TYR 0.019 0.002 TYR D 643 ARG 0.007 0.001 ARG D 503 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 214 time to evaluate : 2.040 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 outliers start: 42 outliers final: 20 residues processed: 241 average time/residue: 0.3418 time to fit residues: 120.2358 Evaluate side-chains 220 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 1.983 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1567 time to fit residues: 8.5841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 HIS C 726 HIS D 319 HIS ** D 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 659 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16884 Z= 0.218 Angle : 0.715 9.252 22884 Z= 0.359 Chirality : 0.045 0.188 2604 Planarity : 0.005 0.062 2972 Dihedral : 6.340 42.074 2324 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 2.26 % Allowed : 16.25 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.05 % 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: -2.33 (0.18), residues: 2120 helix: -0.36 (0.18), residues: 860 sheet: -1.52 (0.32), residues: 233 loop : -2.67 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 292 HIS 0.005 0.001 HIS B 319 PHE 0.038 0.002 PHE D 557 TYR 0.014 0.001 TYR C 505 ARG 0.009 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 217 time to evaluate : 1.919 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 outliers start: 40 outliers final: 11 residues processed: 241 average time/residue: 0.3144 time to fit residues: 111.8795 Evaluate side-chains 203 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 192 time to evaluate : 1.794 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1505 time to fit residues: 5.7781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 6.9990 chunk 116 optimal weight: 0.0870 chunk 2 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 174 optimal weight: 40.0000 chunk 141 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 HIS ** D 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 659 ASN D 664 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16884 Z= 0.216 Angle : 0.707 9.967 22884 Z= 0.354 Chirality : 0.045 0.208 2604 Planarity : 0.005 0.061 2972 Dihedral : 6.069 39.631 2324 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 1.58 % Allowed : 17.38 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.05 % 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: -2.07 (0.18), residues: 2120 helix: -0.12 (0.18), residues: 864 sheet: -1.30 (0.33), residues: 241 loop : -2.58 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 292 HIS 0.005 0.001 HIS B 319 PHE 0.030 0.002 PHE D 557 TYR 0.014 0.001 TYR D 643 ARG 0.005 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 214 time to evaluate : 1.819 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: 28 outliers final: 17 residues processed: 232 average time/residue: 0.3265 time to fit residues: 110.6173 Evaluate side-chains 214 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 197 time to evaluate : 1.953 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1921 time to fit residues: 8.4846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 53.4775 > 50: distance: 1 - 25: 29.140 distance: 5 - 34: 18.967 distance: 12 - 42: 11.903 distance: 21 - 25: 26.667 distance: 22 - 51: 28.443 distance: 25 - 26: 30.108 distance: 26 - 27: 44.406 distance: 26 - 29: 34.377 distance: 27 - 28: 44.826 distance: 27 - 34: 41.707 distance: 28 - 60: 40.311 distance: 29 - 30: 17.667 distance: 30 - 31: 27.729 distance: 31 - 32: 29.027 distance: 32 - 33: 22.962 distance: 34 - 35: 24.075 distance: 35 - 36: 33.613 distance: 35 - 38: 17.418 distance: 36 - 37: 42.613 distance: 36 - 42: 18.274 distance: 38 - 39: 25.391 distance: 38 - 40: 22.717 distance: 39 - 41: 18.185 distance: 42 - 43: 20.979 distance: 43 - 44: 17.102 distance: 43 - 46: 27.543 distance: 44 - 45: 8.732 distance: 44 - 51: 31.787 distance: 46 - 47: 29.296 distance: 47 - 48: 15.222 distance: 48 - 49: 15.120 distance: 48 - 50: 10.847 distance: 51 - 52: 33.042 distance: 52 - 53: 40.668 distance: 52 - 55: 26.859 distance: 53 - 54: 15.434 distance: 53 - 60: 35.066 distance: 55 - 56: 31.042 distance: 56 - 57: 13.276 distance: 57 - 58: 19.158 distance: 57 - 59: 10.655 distance: 60 - 61: 35.854 distance: 61 - 62: 27.509 distance: 61 - 64: 5.244 distance: 62 - 63: 20.862 distance: 62 - 67: 17.021 distance: 64 - 65: 38.613 distance: 64 - 66: 21.377 distance: 67 - 68: 3.892 distance: 68 - 69: 8.306 distance: 69 - 70: 15.224 distance: 72 - 73: 8.096 distance: 72 - 75: 7.963 distance: 73 - 74: 15.343 distance: 73 - 79: 21.413 distance: 75 - 76: 7.429 distance: 76 - 77: 3.623 distance: 77 - 78: 6.526 distance: 79 - 80: 25.202 distance: 79 - 85: 20.071 distance: 80 - 81: 10.884 distance: 80 - 83: 17.711 distance: 81 - 82: 17.428 distance: 81 - 86: 29.575 distance: 82 - 107: 20.830 distance: 83 - 84: 6.385 distance: 84 - 85: 10.639 distance: 86 - 87: 37.360 distance: 87 - 88: 16.910 distance: 87 - 90: 14.144 distance: 88 - 89: 33.889 distance: 88 - 95: 27.825 distance: 89 - 116: 12.754 distance: 90 - 91: 18.250 distance: 91 - 92: 6.576 distance: 92 - 93: 9.279 distance: 92 - 94: 8.900 distance: 95 - 96: 19.261 distance: 96 - 97: 11.147 distance: 96 - 99: 25.341 distance: 97 - 98: 23.888 distance: 97 - 100: 20.860 distance: 98 - 123: 7.231