Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 17:32:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrg_10889/07_2023/6yrg_10889_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrg_10889/07_2023/6yrg_10889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrg_10889/07_2023/6yrg_10889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrg_10889/07_2023/6yrg_10889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrg_10889/07_2023/6yrg_10889_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yrg_10889/07_2023/6yrg_10889_neut.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.100 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 14024 2.51 5 N 3572 2.21 5 O 4336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A GLU 538": "OE1" <-> "OE2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 583": "OD1" <-> "OD2" Residue "A TYR 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 751": "OD1" <-> "OD2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 789": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "B PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B ASP 479": "OD1" <-> "OD2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 533": "NH1" <-> "NH2" Residue "B GLU 534": "OE1" <-> "OE2" Residue "B GLU 545": "OE1" <-> "OE2" Residue "B TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 803": "OE1" <-> "OE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 194": "OD1" <-> "OD2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 533": "NH1" <-> "NH2" Residue "C GLU 538": "OE1" <-> "OE2" Residue "C TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 583": "OD1" <-> "OD2" Residue "C TYR 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 625": "NH1" <-> "NH2" Residue "C PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 751": "OD1" <-> "OD2" Residue "C GLU 764": "OE1" <-> "OE2" Residue "C TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 789": "OE1" <-> "OE2" Residue "D PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 194": "OD1" <-> "OD2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 401": "OE1" <-> "OE2" Residue "D PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "D ASP 479": "OD1" <-> "OD2" Residue "D PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 533": "NH1" <-> "NH2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "D TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 625": "NH1" <-> "NH2" Residue "D TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 803": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 21992 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5498 Classifications: {'peptide': 684} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 662} Chain breaks: 1 Chain: "B" Number of atoms: 5498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5498 Classifications: {'peptide': 684} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 662} Chain breaks: 1 Chain: "C" Number of atoms: 5498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5498 Classifications: {'peptide': 684} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 662} Chain breaks: 1 Chain: "D" Number of atoms: 5498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5498 Classifications: {'peptide': 684} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 662} Chain breaks: 1 Time building chain proxies: 10.62, per 1000 atoms: 0.48 Number of scatterers: 21992 At special positions: 0 Unit cell: (145.905, 152.295, 155.49, 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 4336 8.00 N 3572 7.00 C 14024 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: 9.50 Conformation dependent library (CDL) restraints added in 3.5 seconds 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5184 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 48 sheets defined 31.7% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 105 through 193 Proline residue: A 129 - end of helix Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 215 through 231 Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 257 through 270 Processing helix chain 'A' and resid 276 through 307 Processing helix chain 'A' and resid 313 through 332 Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.836A pdb=" N TYR A 392 " --> pdb=" O LYS A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 531 through 538 removed outlier: 3.611A pdb=" N GLU A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 610 Processing helix chain 'B' and resid 106 through 193 Proline residue: B 129 - end of helix Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 215 through 231 Processing helix chain 'B' and resid 236 through 250 Processing helix chain 'B' and resid 257 through 270 Processing helix chain 'B' and resid 276 through 307 Processing helix chain 'B' and resid 313 through 332 Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 456 through 459 removed outlier: 4.121A pdb=" N GLY B 459 " --> pdb=" O PRO B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 456 through 459' Processing helix chain 'B' and resid 518 through 522 Processing helix chain 'B' and resid 531 through 540 removed outlier: 4.871A pdb=" N GLU B 538 " --> pdb=" O GLU B 534 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 193 Proline residue: C 129 - end of helix Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 215 through 231 Processing helix chain 'C' and resid 236 through 250 Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 276 through 307 Processing helix chain 'C' and resid 313 through 332 Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.837A pdb=" N TYR C 392 " --> pdb=" O LYS C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 412 Processing helix chain 'C' and resid 531 through 538 removed outlier: 3.611A pdb=" N GLU C 538 " --> pdb=" O GLU C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 610 Processing helix chain 'D' and resid 106 through 193 Proline residue: D 129 - end of helix Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 193 through 198 Processing helix chain 'D' and resid 215 through 231 Processing helix chain 'D' and resid 236 through 250 Processing helix chain 'D' and resid 257 through 270 Processing helix chain 'D' and resid 276 through 307 Processing helix chain 'D' and resid 313 through 332 Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 456 through 459 removed outlier: 4.121A pdb=" N GLY D 459 " --> pdb=" O PRO D 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 456 through 459' Processing helix chain 'D' and resid 518 through 522 Processing helix chain 'D' and resid 531 through 540 removed outlier: 4.870A pdb=" N GLU D 538 " --> pdb=" O GLU D 534 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR D 539 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 339 through 341 removed outlier: 3.830A pdb=" N PHE A 340 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 528 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 344 through 348 removed outlier: 4.166A pdb=" N ASN A 348 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE A 495 " --> pdb=" O ASN A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 361 removed outlier: 6.755A pdb=" N THR A 450 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LYS A 465 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 361 removed outlier: 6.894A pdb=" N LYS A 419 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 366 through 374 removed outlier: 5.920A pdb=" N LEU A 368 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA A 386 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY A 370 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR A 384 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE A 403 " --> pdb=" O LYS A 687 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 366 through 374 removed outlier: 5.920A pdb=" N LEU A 368 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA A 386 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY A 370 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR A 384 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE A 403 " --> pdb=" O LYS A 687 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY A 678 " --> pdb=" O LYS A 623 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS A 623 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN A 680 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL A 621 " --> pdb=" O ASN A 680 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN A 615 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 614 " --> pdb=" O SER A 657 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY A 624 " --> pdb=" O ASP A 647 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASP A 647 " --> pdb=" O GLY A 624 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 603 through 605 removed outlier: 6.339A pdb=" N ILE A 628 " --> pdb=" O GLU A 639 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU A 639 " --> pdb=" O ILE A 628 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 630 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 603 through 605 Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.681A pdb=" N GLN A 725 " --> pdb=" O ILE A 781 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 781 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 782 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER A 748 " --> pdb=" O ALA A 782 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 747 " --> pdb=" O VAL A 759 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL A 759 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 749 " --> pdb=" O LEU A 757 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 707 through 708 removed outlier: 4.116A pdb=" N GLN A 708 " --> pdb=" O GLU A 716 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 716 " --> pdb=" O GLN A 708 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 736 through 738 removed outlier: 3.760A pdb=" N LEU A 737 " --> pdb=" O ARG A 768 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 768 " --> pdb=" O LEU A 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 344 through 348 removed outlier: 3.816A pdb=" N ASN B 348 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 495 " --> pdb=" O ASN B 348 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 357 through 361 removed outlier: 5.071A pdb=" N TYR B 431 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR B 454 " --> pdb=" O TYR B 431 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE B 433 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN B 452 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS B 435 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 450 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 441 " --> pdb=" O GLN B 444 " (cutoff:3.500A) removed outlier: 12.476A pdb=" N TYR B 447 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 11.073A pdb=" N VAL B 468 " --> pdb=" O TYR B 447 " (cutoff:3.500A) removed outlier: 11.703A pdb=" N VAL B 449 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N VAL B 466 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N ALA B 451 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ASN B 464 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE B 453 " --> pdb=" O ASP B 462 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 357 through 361 removed outlier: 5.071A pdb=" N TYR B 431 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR B 454 " --> pdb=" O TYR B 431 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE B 433 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN B 452 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS B 435 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 450 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 441 " --> pdb=" O GLN B 444 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR B 421 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N TYR B 447 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 366 through 370 removed outlier: 6.162A pdb=" N TYR B 384 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 373 through 374 removed outlier: 4.654A pdb=" N LEU B 381 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 424 through 426 Processing sheet with id=AB9, first strand: chain 'B' and resid 574 through 575 removed outlier: 3.749A pdb=" N TYR B 629 " --> pdb=" O LEU B 667 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 596 through 597 Processing sheet with id=AC2, first strand: chain 'B' and resid 645 through 649 removed outlier: 5.468A pdb=" N ASP B 647 " --> pdb=" O ILE B 622 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE B 622 " --> pdb=" O ASP B 647 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN B 649 " --> pdb=" O TYR B 620 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR B 620 " --> pdb=" O GLN B 649 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 614 " --> pdb=" O SER B 657 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 655 " --> pdb=" O TYR B 616 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 618 " --> pdb=" O LYS B 653 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 645 through 649 removed outlier: 5.468A pdb=" N ASP B 647 " --> pdb=" O ILE B 622 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE B 622 " --> pdb=" O ASP B 647 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN B 649 " --> pdb=" O TYR B 620 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR B 620 " --> pdb=" O GLN B 649 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 615 " --> pdb=" O ILE B 686 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 621 " --> pdb=" O ASN B 680 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN B 680 " --> pdb=" O VAL B 621 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 701 through 703 removed outlier: 3.910A pdb=" N GLN B 725 " --> pdb=" O ILE B 781 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 781 " --> pdb=" O GLN B 725 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 757 " --> pdb=" O ILE B 749 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 716 through 717 Processing sheet with id=AC6, first strand: chain 'B' and resid 769 through 770 removed outlier: 3.770A pdb=" N THR B 734 " --> pdb=" O GLU B 803 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 339 through 341 removed outlier: 3.831A pdb=" N PHE C 340 " --> pdb=" O GLY C 528 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 528 " --> pdb=" O PHE C 340 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 344 through 348 removed outlier: 4.167A pdb=" N ASN C 348 " --> pdb=" O ILE C 495 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE C 495 " --> pdb=" O ASN C 348 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 357 through 361 removed outlier: 6.755A pdb=" N THR C 450 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS C 465 " --> pdb=" O PHE C 453 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 357 through 361 removed outlier: 6.894A pdb=" N LYS C 419 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 366 through 374 removed outlier: 5.921A pdb=" N LEU C 368 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA C 386 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY C 370 " --> pdb=" O TYR C 384 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR C 384 " --> pdb=" O GLY C 370 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE C 403 " --> pdb=" O LYS C 687 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 366 through 374 removed outlier: 5.921A pdb=" N LEU C 368 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA C 386 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY C 370 " --> pdb=" O TYR C 384 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR C 384 " --> pdb=" O GLY C 370 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE C 403 " --> pdb=" O LYS C 687 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY C 678 " --> pdb=" O LYS C 623 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS C 623 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN C 680 " --> pdb=" O VAL C 621 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL C 621 " --> pdb=" O ASN C 680 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN C 615 " --> pdb=" O ILE C 686 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR C 614 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY C 624 " --> pdb=" O ASP C 647 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASP C 647 " --> pdb=" O GLY C 624 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 603 through 605 removed outlier: 6.339A pdb=" N ILE C 628 " --> pdb=" O GLU C 639 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU C 639 " --> pdb=" O ILE C 628 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C 630 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 603 through 605 Processing sheet with id=AD6, first strand: chain 'C' and resid 702 through 704 removed outlier: 3.681A pdb=" N GLN C 725 " --> pdb=" O ILE C 781 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 781 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA C 782 " --> pdb=" O SER C 748 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER C 748 " --> pdb=" O ALA C 782 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 747 " --> pdb=" O VAL C 759 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL C 759 " --> pdb=" O VAL C 747 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE C 749 " --> pdb=" O LEU C 757 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 707 through 708 removed outlier: 4.117A pdb=" N GLN C 708 " --> pdb=" O GLU C 716 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU C 716 " --> pdb=" O GLN C 708 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 736 through 738 removed outlier: 3.760A pdb=" N LEU C 737 " --> pdb=" O ARG C 768 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 768 " --> pdb=" O LEU C 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 344 through 348 removed outlier: 3.815A pdb=" N ASN D 348 " --> pdb=" O ILE D 495 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE D 495 " --> pdb=" O ASN D 348 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 357 through 361 removed outlier: 5.072A pdb=" N TYR D 431 " --> pdb=" O TYR D 454 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR D 454 " --> pdb=" O TYR D 431 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE D 433 " --> pdb=" O ASN D 452 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN D 452 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS D 435 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 450 " --> pdb=" O LYS D 435 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG D 441 " --> pdb=" O GLN D 444 " (cutoff:3.500A) removed outlier: 12.476A pdb=" N TYR D 447 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 11.073A pdb=" N VAL D 468 " --> pdb=" O TYR D 447 " (cutoff:3.500A) removed outlier: 11.704A pdb=" N VAL D 449 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N VAL D 466 " --> pdb=" O VAL D 449 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N ALA D 451 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ASN D 464 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE D 453 " --> pdb=" O ASP D 462 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 357 through 361 removed outlier: 5.072A pdb=" N TYR D 431 " --> pdb=" O TYR D 454 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR D 454 " --> pdb=" O TYR D 431 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE D 433 " --> pdb=" O ASN D 452 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN D 452 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS D 435 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 450 " --> pdb=" O LYS D 435 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG D 441 " --> pdb=" O GLN D 444 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR D 421 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR D 447 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 366 through 370 removed outlier: 6.161A pdb=" N TYR D 384 " --> pdb=" O ILE D 369 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 373 through 374 removed outlier: 4.653A pdb=" N LEU D 381 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 424 through 426 Processing sheet with id=AE6, first strand: chain 'D' and resid 574 through 575 removed outlier: 3.748A pdb=" N TYR D 629 " --> pdb=" O LEU D 667 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 596 through 597 Processing sheet with id=AE8, first strand: chain 'D' and resid 645 through 649 removed outlier: 5.468A pdb=" N ASP D 647 " --> pdb=" O ILE D 622 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE D 622 " --> pdb=" O ASP D 647 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN D 649 " --> pdb=" O TYR D 620 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR D 620 " --> pdb=" O GLN D 649 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR D 614 " --> pdb=" O SER D 657 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE D 655 " --> pdb=" O TYR D 616 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 618 " --> pdb=" O LYS D 653 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 645 through 649 removed outlier: 5.468A pdb=" N ASP D 647 " --> pdb=" O ILE D 622 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE D 622 " --> pdb=" O ASP D 647 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN D 649 " --> pdb=" O TYR D 620 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR D 620 " --> pdb=" O GLN D 649 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN D 615 " --> pdb=" O ILE D 686 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 621 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN D 680 " --> pdb=" O VAL D 621 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 701 through 703 removed outlier: 3.910A pdb=" N GLN D 725 " --> pdb=" O ILE D 781 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 781 " --> pdb=" O GLN D 725 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU D 757 " --> pdb=" O ILE D 749 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 716 through 717 Processing sheet with id=AF3, first strand: chain 'D' and resid 769 through 770 removed outlier: 3.771A pdb=" N THR D 734 " --> pdb=" O GLU D 803 " (cutoff:3.500A) 1033 hydrogen bonds defined for protein. 2871 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: 9.44 Time building geometry restraints manager: 10.15 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: 6129 1.34 - 1.46: 5891 1.46 - 1.58: 10276 1.58 - 1.71: 4 1.71 - 1.83: 100 Bond restraints: 22400 Sorted by residual: bond pdb=" N LEU A 336 " pdb=" CA LEU A 336 " ideal model delta sigma weight residual 1.457 1.570 -0.112 1.29e-02 6.01e+03 7.57e+01 bond pdb=" N LEU C 336 " pdb=" CA LEU C 336 " ideal model delta sigma weight residual 1.457 1.568 -0.111 1.29e-02 6.01e+03 7.42e+01 bond pdb=" C LEU B 336 " pdb=" N SER B 337 " ideal model delta sigma weight residual 1.331 1.425 -0.095 1.23e-02 6.61e+03 5.92e+01 bond pdb=" C LEU D 336 " pdb=" N SER D 337 " ideal model delta sigma weight residual 1.331 1.424 -0.093 1.23e-02 6.61e+03 5.75e+01 bond pdb=" N THR C 335 " pdb=" CA THR C 335 " ideal model delta sigma weight residual 1.454 1.543 -0.089 1.23e-02 6.61e+03 5.28e+01 ... (remaining 22395 not shown) Histogram of bond angle deviations from ideal: 93.97 - 102.34: 63 102.34 - 110.72: 6246 110.72 - 119.09: 12048 119.09 - 127.46: 11805 127.46 - 135.83: 146 Bond angle restraints: 30308 Sorted by residual: angle pdb=" O PRO A 334 " pdb=" C PRO A 334 " pdb=" N THR A 335 " ideal model delta sigma weight residual 122.64 105.61 17.03 1.35e+00 5.49e-01 1.59e+02 angle pdb=" O PRO C 334 " pdb=" C PRO C 334 " pdb=" N THR C 335 " ideal model delta sigma weight residual 122.64 105.75 16.89 1.35e+00 5.49e-01 1.57e+02 angle pdb=" C THR B 335 " pdb=" CA THR B 335 " pdb=" CB THR B 335 " ideal model delta sigma weight residual 110.42 134.84 -24.42 1.99e+00 2.53e-01 1.51e+02 angle pdb=" C THR D 335 " pdb=" CA THR D 335 " pdb=" CB THR D 335 " ideal model delta sigma weight residual 110.42 133.61 -23.19 1.99e+00 2.53e-01 1.36e+02 angle pdb=" CA THR A 335 " pdb=" C THR A 335 " pdb=" O THR A 335 " ideal model delta sigma weight residual 121.11 109.36 11.75 1.13e+00 7.83e-01 1.08e+02 ... (remaining 30303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 12299 17.66 - 35.33: 1035 35.33 - 52.99: 182 52.99 - 70.66: 36 70.66 - 88.32: 12 Dihedral angle restraints: 13564 sinusoidal: 5524 harmonic: 8040 Sorted by residual: dihedral pdb=" CA THR B 335 " pdb=" C THR B 335 " pdb=" N LEU B 336 " pdb=" CA LEU B 336 " ideal model delta harmonic sigma weight residual 180.00 -114.21 -65.79 0 5.00e+00 4.00e-02 1.73e+02 dihedral pdb=" CA THR D 335 " pdb=" C THR D 335 " pdb=" N LEU D 336 " pdb=" CA LEU D 336 " ideal model delta harmonic sigma weight residual -180.00 -114.78 -65.22 0 5.00e+00 4.00e-02 1.70e+02 dihedral pdb=" C THR B 335 " pdb=" N THR B 335 " pdb=" CA THR B 335 " pdb=" CB THR B 335 " ideal model delta harmonic sigma weight residual -122.00 -146.73 24.73 0 2.50e+00 1.60e-01 9.78e+01 ... (remaining 13561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 3251 0.150 - 0.300: 161 0.300 - 0.450: 21 0.450 - 0.600: 5 0.600 - 0.751: 2 Chirality restraints: 3440 Sorted by residual: chirality pdb=" CA THR B 335 " pdb=" N THR B 335 " pdb=" C THR B 335 " pdb=" CB THR B 335 " both_signs ideal model delta sigma weight residual False 2.53 1.78 0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" CA THR D 335 " pdb=" N THR D 335 " pdb=" C THR D 335 " pdb=" CB THR D 335 " both_signs ideal model delta sigma weight residual False 2.53 1.88 0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CA THR B 180 " pdb=" N THR B 180 " pdb=" C THR B 180 " pdb=" CB THR B 180 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.47 2.00e-01 2.50e+01 5.42e+00 ... (remaining 3437 not shown) Planarity restraints: 3892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 334 " 0.086 2.00e-02 2.50e+03 1.77e-01 3.14e+02 pdb=" C PRO D 334 " -0.306 2.00e-02 2.50e+03 pdb=" O PRO D 334 " 0.125 2.00e-02 2.50e+03 pdb=" N THR D 335 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 334 " -0.085 2.00e-02 2.50e+03 1.75e-01 3.08e+02 pdb=" C PRO B 334 " 0.303 2.00e-02 2.50e+03 pdb=" O PRO B 334 " -0.123 2.00e-02 2.50e+03 pdb=" N THR B 335 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 334 " 0.086 2.00e-02 2.50e+03 1.55e-01 2.41e+02 pdb=" C PRO A 334 " -0.268 2.00e-02 2.50e+03 pdb=" O PRO A 334 " 0.099 2.00e-02 2.50e+03 pdb=" N THR A 335 " 0.084 2.00e-02 2.50e+03 ... (remaining 3889 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 12 2.00 - 2.72: 1394 2.72 - 3.45: 35339 3.45 - 4.17: 59931 4.17 - 4.90: 101166 Nonbonded interactions: 197842 Sorted by model distance: nonbonded pdb=" O ILE B 332 " pdb=" CG2 THR B 335 " model vdw 1.270 3.460 nonbonded pdb=" O ILE D 332 " pdb=" CG2 THR D 335 " model vdw 1.324 3.460 nonbonded pdb=" O LEU D 333 " pdb=" OG1 THR D 335 " model vdw 1.500 2.440 nonbonded pdb=" O LEU B 333 " pdb=" OG1 THR B 335 " model vdw 1.657 2.440 nonbonded pdb=" NZ LYS B 325 " pdb=" ND2 ASN B 543 " model vdw 1.777 3.200 ... (remaining 197837 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 Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 7.870 Check model and map are aligned: 0.310 Set scattering table: 0.230 Process input model: 59.510 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.100 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3241 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 : 0.009 0.112 22400 Z= 0.596 Angle : 1.413 24.415 30308 Z= 0.952 Chirality : 0.081 0.751 3440 Planarity : 0.010 0.177 3892 Dihedral : 13.689 88.322 8380 Min Nonbonded Distance : 1.270 Molprobity Statistics. All-atom Clashscore : 31.61 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.38 % Favored : 90.33 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.26 (0.16), residues: 2720 helix: 2.81 (0.17), residues: 780 sheet: -3.12 (0.20), residues: 538 loop : -3.58 (0.13), residues: 1402 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5440 Ramachandran restraints generated. 2720 Oldfield, 0 Emsley, 2720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.708 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: 4 outliers final: 1 residues processed: 96 average time/residue: 0.2649 time to fit residues: 31.0900 Evaluate side-chains 44 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.676 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0564 time to fit residues: 0.9926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 0.0050 chunk 206 optimal weight: 20.0000 chunk 114 optimal weight: 0.0870 chunk 70 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 110 optimal weight: 0.4980 chunk 213 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 129 optimal weight: 0.0270 chunk 158 optimal weight: 3.9990 chunk 247 optimal weight: 0.0010 overall best weight: 0.1236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 GLN C 242 GLN C 319 HIS ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN C 569 ASN ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2972 moved from start: 1.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.374 22400 Z= 0.771 Angle : 1.245 30.721 30308 Z= 0.732 Chirality : 0.077 0.976 3440 Planarity : 0.006 0.054 3892 Dihedral : 7.219 50.017 2928 Min Nonbonded Distance : 1.144 Molprobity Statistics. All-atom Clashscore : 38.71 Ramachandran Plot: Outliers : 2.50 % Allowed : 9.56 % Favored : 87.94 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.92 (0.16), residues: 2720 helix: 1.98 (0.19), residues: 768 sheet: -2.00 (0.22), residues: 580 loop : -3.02 (0.14), residues: 1372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.2352 time to fit residues: 21.9670 Evaluate side-chains 38 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 50.0000 chunk 76 optimal weight: 4.9990 chunk 205 optimal weight: 50.0000 chunk 168 optimal weight: 7.9990 chunk 68 optimal weight: 50.0000 chunk 247 optimal weight: 20.0000 chunk 267 optimal weight: 0.8980 chunk 220 optimal weight: 0.6980 chunk 245 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 GLN C 348 ASN C 375 ASN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3267 moved from start: 1.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.329 22400 Z= 0.791 Angle : 1.135 28.534 30308 Z= 0.677 Chirality : 0.068 0.878 3440 Planarity : 0.006 0.057 3892 Dihedral : 6.810 55.782 2928 Min Nonbonded Distance : 1.145 Molprobity Statistics. All-atom Clashscore : 35.38 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.59 % Favored : 88.82 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.25 (0.15), residues: 2720 helix: 1.30 (0.19), residues: 756 sheet: -2.03 (0.20), residues: 652 loop : -3.01 (0.14), residues: 1312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.1914 time to fit residues: 16.9512 Evaluate side-chains 45 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.660 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 1.9990 chunk 186 optimal weight: 0.1980 chunk 128 optimal weight: 0.0570 chunk 27 optimal weight: 0.0270 chunk 118 optimal weight: 0.0010 chunk 166 optimal weight: 0.0010 chunk 248 optimal weight: 0.0040 chunk 262 optimal weight: 0.9990 chunk 129 optimal weight: 0.0270 chunk 235 optimal weight: 0.3980 chunk 70 optimal weight: 30.0000 overall best weight: 0.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 GLN C 270 ASN C 324 GLN C 375 ASN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN C 633 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3115 moved from start: 1.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.394 22400 Z= 0.807 Angle : 1.201 29.719 30308 Z= 0.712 Chirality : 0.066 0.893 3440 Planarity : 0.006 0.081 3892 Dihedral : 6.396 48.354 2928 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 26.46 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.18 % Favored : 88.53 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.44 (0.15), residues: 2720 helix: 0.30 (0.18), residues: 780 sheet: -1.60 (0.21), residues: 588 loop : -2.89 (0.14), residues: 1352 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.2399 time to fit residues: 19.4433 Evaluate side-chains 41 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.704 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 0.4980 chunk 149 optimal weight: 0.0470 chunk 3 optimal weight: 10.0000 chunk 195 optimal weight: 20.0000 chunk 108 optimal weight: 0.0030 chunk 224 optimal weight: 0.6980 chunk 181 optimal weight: 0.0970 chunk 0 optimal weight: 40.0000 chunk 134 optimal weight: 10.0000 chunk 235 optimal weight: 0.0370 chunk 66 optimal weight: 9.9990 overall best weight: 0.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3140 moved from start: 1.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.175 22400 Z= 0.377 Angle : 1.263 62.300 30308 Z= 0.604 Chirality : 0.052 0.560 3440 Planarity : 0.005 0.059 3892 Dihedral : 5.868 35.443 2928 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 23.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.88 % Favored : 88.97 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.03 (0.15), residues: 2720 helix: 0.68 (0.18), residues: 792 sheet: -1.24 (0.22), residues: 636 loop : -2.80 (0.14), residues: 1292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.2262 time to fit residues: 15.7163 Evaluate side-chains 39 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.660 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 0.8980 chunk 236 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 154 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 263 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 121 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 ASN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3174 moved from start: 1.6712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.178 22400 Z= 0.323 Angle : 1.167 63.693 30308 Z= 0.555 Chirality : 0.054 0.538 3440 Planarity : 0.005 0.061 3892 Dihedral : 5.734 31.505 2928 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.59 % Favored : 89.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.01 (0.16), residues: 2720 helix: 0.62 (0.19), residues: 792 sheet: -1.14 (0.22), residues: 636 loop : -2.79 (0.15), residues: 1292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2134 time to fit residues: 13.9949 Evaluate side-chains 41 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.665 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 0.0980 chunk 29 optimal weight: 0.7980 chunk 149 optimal weight: 0.4980 chunk 192 optimal weight: 0.0370 chunk 148 optimal weight: 0.9980 chunk 221 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 262 optimal weight: 0.0170 chunk 164 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 106 GLN C 111 ASN C 118 ASN C 121 ASN C 375 ASN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3162 moved from start: 1.7004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 22400 Z= 0.208 Angle : 0.845 37.481 30308 Z= 0.424 Chirality : 0.047 0.356 3440 Planarity : 0.004 0.040 3892 Dihedral : 5.423 26.524 2928 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.32 % Favored : 88.53 % Rotamer Outliers : 0.00 % 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: -1.89 (0.16), residues: 2720 helix: 0.75 (0.18), residues: 796 sheet: -1.12 (0.22), residues: 632 loop : -2.71 (0.15), residues: 1292 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2300 time to fit residues: 16.8236 Evaluate side-chains 39 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 0.3980 chunk 104 optimal weight: 0.8980 chunk 156 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 0.0970 chunk 166 optimal weight: 0.0970 chunk 178 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN C 375 ASN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3204 moved from start: 1.7267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 22400 Z= 0.163 Angle : 0.689 10.812 30308 Z= 0.377 Chirality : 0.044 0.181 3440 Planarity : 0.004 0.037 3892 Dihedral : 5.167 23.347 2928 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.71 % Favored : 90.15 % Rotamer Outliers : 0.00 % 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: -1.75 (0.16), residues: 2720 helix: 1.02 (0.18), residues: 780 sheet: -1.19 (0.22), residues: 652 loop : -2.61 (0.15), residues: 1288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1941 time to fit residues: 13.7485 Evaluate side-chains 38 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.644 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 0.3980 chunk 251 optimal weight: 0.0980 chunk 229 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 147 optimal weight: 0.0060 chunk 106 optimal weight: 6.9990 chunk 191 optimal weight: 0.0170 chunk 74 optimal weight: 0.9980 chunk 220 optimal weight: 0.7980 chunk 231 optimal weight: 0.0470 chunk 243 optimal weight: 0.8980 overall best weight: 0.1132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 375 ASN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3178 moved from start: 1.7570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 22400 Z= 0.158 Angle : 0.678 7.294 30308 Z= 0.372 Chirality : 0.044 0.186 3440 Planarity : 0.004 0.037 3892 Dihedral : 4.962 21.620 2928 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.71 % Favored : 90.15 % Rotamer Outliers : 0.00 % 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: -1.57 (0.16), residues: 2720 helix: 1.29 (0.18), residues: 764 sheet: -0.89 (0.22), residues: 616 loop : -2.64 (0.15), residues: 1340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2144 time to fit residues: 15.3840 Evaluate side-chains 37 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.691 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 270 optimal weight: 0.0870 chunk 249 optimal weight: 0.1980 chunk 215 optimal weight: 0.0970 chunk 22 optimal weight: 2.9990 chunk 166 optimal weight: 0.3980 chunk 132 optimal weight: 9.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 375 ASN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3217 moved from start: 1.7740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 22400 Z= 0.153 Angle : 0.694 10.547 30308 Z= 0.373 Chirality : 0.045 0.183 3440 Planarity : 0.004 0.043 3892 Dihedral : 4.800 21.689 2928 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.71 % Favored : 90.15 % Rotamer Outliers : 0.00 % 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: -1.45 (0.16), residues: 2720 helix: 1.42 (0.18), residues: 764 sheet: -0.78 (0.22), residues: 616 loop : -2.61 (0.15), residues: 1340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2267 time to fit residues: 16.1436 Evaluate side-chains 40 residues out of total 626 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.694 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 198 optimal weight: 0.0570 chunk 31 optimal weight: 0.0010 chunk 59 optimal weight: 6.9990 chunk 216 optimal weight: 0.6980 chunk 90 optimal weight: 0.0570 chunk 221 optimal weight: 0.0980 chunk 27 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 375 ASN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 577 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.128775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.107014 restraints weight = 49946.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.107692 restraints weight = 32040.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.107876 restraints weight = 25820.706| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4911 moved from start: 1.7934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 22400 Z= 0.152 Angle : 0.678 6.747 30308 Z= 0.369 Chirality : 0.044 0.190 3440 Planarity : 0.004 0.044 3892 Dihedral : 4.711 20.673 2928 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.71 % Favored : 90.15 % Rotamer Outliers : 0.00 % 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: -1.41 (0.16), residues: 2720 helix: 1.31 (0.18), residues: 764 sheet: -0.64 (0.23), residues: 616 loop : -2.55 (0.15), residues: 1340 =============================================================================== Job complete usr+sys time: 2782.80 seconds wall clock time: 53 minutes 9.59 seconds (3189.59 seconds total)