Starting phenix.real_space_refine (version: dev) on Sun May 15 10:17:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/05_2022/6acd_9589.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/05_2022/6acd_9589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/05_2022/6acd_9589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/05_2022/6acd_9589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/05_2022/6acd_9589.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/05_2022/6acd_9589.pdb" } resolution = 3.9 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= -0.002 sd= 0.873 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1001": "NH1" <-> "NH2" Residue "A ARG 1021": "NH1" <-> "NH2" Residue "A ARG 1073": "NH1" <-> "NH2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1001": "NH1" <-> "NH2" Residue "B ARG 1021": "NH1" <-> "NH2" Residue "B ARG 1073": "NH1" <-> "NH2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1001": "NH1" <-> "NH2" Residue "C ARG 1021": "NH1" <-> "NH2" Residue "C PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1073": "NH1" <-> "NH2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 24845 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 50, 'TRANS': 1013, 'PCIS': 1} Chain breaks: 3 Chain: "B" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8302 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 50, 'TRANS': 1013, 'PCIS': 1} Chain breaks: 3 Chain: "C" Number of atoms: 8241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8241 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 49, 'TRANS': 1006, 'PCIS': 1} Chain breaks: 5 Time building chain proxies: 12.87, per 1000 atoms: 0.52 Number of scatterers: 24845 At special positions: 0 Unit cell: (146.52, 146.52, 179.52, 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 135 16.00 O 4726 8.00 N 4112 7.00 C 15872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.02 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.04 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.01 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.02 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.04 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.02 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.02 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.04 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.02 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.02 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.04 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.01 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.74 Conformation dependent library (CDL) restraints added in 4.0 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5972 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 44 sheets defined 20.2% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.513A pdb=" N LEU A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A 376 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 377 " --> pdb=" O LEU A 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 371 through 377' Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.555A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 808 Processing helix chain 'A' and resid 848 through 865 Processing helix chain 'A' and resid 880 through 888 removed outlier: 3.580A pdb=" N MET A 884 " --> pdb=" O PHE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 900 removed outlier: 3.884A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 removed outlier: 3.906A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 950 removed outlier: 4.312A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1017 removed outlier: 3.753A pdb=" N VAL A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1016 " --> pdb=" O SER A1012 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A1017 " --> pdb=" O GLU A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 373 through 377 removed outlier: 3.898A pdb=" N ASP B 376 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 373 through 377' Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 604 through 611 removed outlier: 3.706A pdb=" N THR B 608 " --> pdb=" O THR B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 737 Processing helix chain 'B' and resid 740 through 765 Processing helix chain 'B' and resid 798 through 808 Processing helix chain 'B' and resid 848 through 865 Processing helix chain 'B' and resid 880 through 887 removed outlier: 3.545A pdb=" N MET B 884 " --> pdb=" O PHE B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.877A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 removed outlier: 4.151A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 950 removed outlier: 4.083A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 1014 Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 371 through 375 removed outlier: 3.546A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 371 through 375' Processing helix chain 'C' and resid 390 through 397 removed outlier: 4.513A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.547A pdb=" N TYR C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 612 Processing helix chain 'C' and resid 730 through 737 Processing helix chain 'C' and resid 740 through 764 Processing helix chain 'C' and resid 798 through 808 Processing helix chain 'C' and resid 848 through 865 Processing helix chain 'C' and resid 880 through 888 removed outlier: 3.687A pdb=" N MET C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 900 Processing helix chain 'C' and resid 901 through 922 removed outlier: 4.010A pdb=" N THR C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 950 removed outlier: 4.142A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 1014 removed outlier: 4.000A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.627A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.781A pdb=" N THR A 260 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.939A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 141 removed outlier: 5.472A pdb=" N ALA A 237 " --> pdb=" O VAL A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 298 through 306 removed outlier: 4.107A pdb=" N THR A 585 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 302 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 628 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.538A pdb=" N ASN A 526 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 539 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 345 Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.385A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB1, first strand: chain 'A' and resid 640 through 642 removed outlier: 5.557A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 650 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 683 through 684 removed outlier: 6.015A pdb=" N ALA A 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 700 through 701 removed outlier: 3.603A pdb=" N VAL A1050 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 704 through 710 removed outlier: 3.626A pdb=" N GLU A 707 " --> pdb=" O PHE A1044 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB6, first strand: chain 'A' and resid 769 through 770 removed outlier: 6.158A pdb=" N ALA B 683 " --> pdb=" O MET A 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB8, first strand: chain 'A' and resid 1069 through 1071 removed outlier: 3.689A pdb=" N PHE A1071 " --> pdb=" O PHE A1103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1078 through 1079 Processing sheet with id=AC1, first strand: chain 'B' and resid 31 through 34 removed outlier: 4.191A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 252 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS B 181 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 184 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.908A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 81 through 82 removed outlier: 7.020A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 139 through 141 removed outlier: 6.433A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 300 through 306 removed outlier: 5.838A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER B 303 " --> pdb=" O VAL B 581 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 341 through 345 Processing sheet with id=AC7, first strand: chain 'B' and resid 440 through 441 Processing sheet with id=AC8, first strand: chain 'B' and resid 525 through 528 removed outlier: 4.093A pdb=" N GLY B 534 " --> pdb=" O PHE B 527 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 539 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.999A pdb=" N ILE B 650 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 658 " --> pdb=" O ILE B 650 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 700 through 701 Processing sheet with id=AD2, first strand: chain 'B' and resid 704 through 710 Processing sheet with id=AD3, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD4, first strand: chain 'B' and resid 1078 through 1079 removed outlier: 3.527A pdb=" N GLN B1095 " --> pdb=" O ILE B1086 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.507A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR C 252 " --> pdb=" O PHE C 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 71 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA C 250 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 51 through 59 removed outlier: 4.157A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 81 through 82 removed outlier: 7.168A pdb=" N ASN C 129 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS C 159 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 139 through 141 removed outlier: 5.453A pdb=" N ALA C 237 " --> pdb=" O VAL C 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 300 through 306 removed outlier: 4.471A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.629A pdb=" N GLY C 534 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP C 560 " --> pdb=" O ASP C 572 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 341 through 345 Processing sheet with id=AE3, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE4, first strand: chain 'C' and resid 650 through 652 removed outlier: 3.555A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 704 through 710 removed outlier: 3.668A pdb=" N ALA C1038 " --> pdb=" O GLY C1041 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AE7, first strand: chain 'C' and resid 1069 through 1071 removed outlier: 3.665A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE C1071 " --> pdb=" O PHE C1103 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE C1103 " --> pdb=" O PHE C1071 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1078 through 1079 844 hydrogen bonds defined for protein. 2310 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: 10.21 Time building geometry restraints manager: 11.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7362 1.33 - 1.46: 6117 1.46 - 1.58: 11771 1.58 - 1.71: 0 1.71 - 1.83: 183 Bond restraints: 25433 Sorted by residual: bond pdb=" C PHE C 316 " pdb=" N PRO C 317 " ideal model delta sigma weight residual 1.331 1.368 -0.036 1.21e-02 6.83e+03 8.96e+00 bond pdb=" CA THR C 517 " pdb=" C THR C 517 " ideal model delta sigma weight residual 1.525 1.466 0.059 2.10e-02 2.27e+03 7.79e+00 bond pdb=" CB CYS B 725 " pdb=" SG CYS B 725 " ideal model delta sigma weight residual 1.808 1.740 0.068 3.30e-02 9.18e+02 4.29e+00 bond pdb=" C LYS C 142 " pdb=" N PRO C 143 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.94e+00 bond pdb=" C LYS B 142 " pdb=" N PRO B 143 " ideal model delta sigma weight residual 1.332 1.349 -0.017 8.90e-03 1.26e+04 3.55e+00 ... (remaining 25428 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.26: 545 105.26 - 112.47: 12701 112.47 - 119.67: 8229 119.67 - 126.87: 12869 126.87 - 134.08: 269 Bond angle restraints: 34613 Sorted by residual: angle pdb=" N THR C 517 " pdb=" CA THR C 517 " pdb=" C THR C 517 " ideal model delta sigma weight residual 111.00 131.24 -20.24 2.80e+00 1.28e-01 5.22e+01 angle pdb=" N ILE C 891 " pdb=" CA ILE C 891 " pdb=" C ILE C 891 " ideal model delta sigma weight residual 113.71 107.02 6.69 9.50e-01 1.11e+00 4.96e+01 angle pdb=" C THR C 517 " pdb=" N ASP C 518 " pdb=" CA ASP C 518 " ideal model delta sigma weight residual 121.54 108.48 13.06 1.91e+00 2.74e-01 4.67e+01 angle pdb=" N GLY A 634 " pdb=" CA GLY A 634 " pdb=" C GLY A 634 " ideal model delta sigma weight residual 111.63 117.99 -6.36 1.15e+00 7.56e-01 3.06e+01 angle pdb=" C LYS B 968 " pdb=" N VAL B 969 " pdb=" CA VAL B 969 " ideal model delta sigma weight residual 120.62 129.43 -8.81 1.64e+00 3.72e-01 2.89e+01 ... (remaining 34608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 14522 17.87 - 35.74: 469 35.74 - 53.60: 96 53.60 - 71.47: 24 71.47 - 89.34: 8 Dihedral angle restraints: 15119 sinusoidal: 5833 harmonic: 9286 Sorted by residual: dihedral pdb=" CA GLU A1074 " pdb=" C GLU A1074 " pdb=" N GLY A1075 " pdb=" CA GLY A1075 " ideal model delta harmonic sigma weight residual -180.00 -109.21 -70.79 0 5.00e+00 4.00e-02 2.00e+02 dihedral pdb=" CA GLU C1074 " pdb=" C GLU C1074 " pdb=" N GLY C1075 " pdb=" CA GLY C1075 " ideal model delta harmonic sigma weight residual -180.00 -113.59 -66.41 0 5.00e+00 4.00e-02 1.76e+02 dihedral pdb=" CB CYS B 725 " pdb=" SG CYS B 725 " pdb=" SG CYS B 731 " pdb=" CB CYS B 731 " ideal model delta sinusoidal sigma weight residual -86.00 -175.34 89.34 1 1.00e+01 1.00e-02 9.49e+01 ... (remaining 15116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 3818 0.140 - 0.280: 99 0.280 - 0.420: 0 0.420 - 0.560: 0 0.560 - 0.700: 1 Chirality restraints: 3918 Sorted by residual: chirality pdb=" CA THR C 517 " pdb=" N THR C 517 " pdb=" C THR C 517 " pdb=" CB THR C 517 " both_signs ideal model delta sigma weight residual False 2.53 1.83 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CG LEU A 745 " pdb=" CB LEU A 745 " pdb=" CD1 LEU A 745 " pdb=" CD2 LEU A 745 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB THR A 71 " pdb=" CA THR A 71 " pdb=" OG1 THR A 71 " pdb=" CG2 THR A 71 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 3915 not shown) Planarity restraints: 4485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 678 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C THR A 678 " 0.058 2.00e-02 2.50e+03 pdb=" O THR A 678 " -0.022 2.00e-02 2.50e+03 pdb=" N MET A 679 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 678 " 0.016 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C THR B 678 " -0.057 2.00e-02 2.50e+03 pdb=" O THR B 678 " 0.021 2.00e-02 2.50e+03 pdb=" N MET B 679 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 517 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C THR C 517 " 0.056 2.00e-02 2.50e+03 pdb=" O THR C 517 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP C 518 " -0.018 2.00e-02 2.50e+03 ... (remaining 4482 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 5 2.28 - 2.94: 11203 2.94 - 3.59: 34304 3.59 - 4.25: 56511 4.25 - 4.90: 92829 Nonbonded interactions: 194852 Sorted by model distance: nonbonded pdb=" O VAL C 314 " pdb=" CG2 THR C 517 " model vdw 1.629 3.460 nonbonded pdb=" OG SER A 95 " pdb=" O SER A 173 " model vdw 2.242 2.440 nonbonded pdb=" O GLN C 939 " pdb=" OG1 THR C 943 " model vdw 2.246 2.440 nonbonded pdb=" OG SER C 95 " pdb=" O SER C 173 " model vdw 2.262 2.440 nonbonded pdb=" OG SER B 95 " pdb=" O SER B 173 " model vdw 2.281 2.440 ... (remaining 194847 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 318 or resid 323 through 512 or resid 517 throu \ gh 1119)) selection = (chain 'B' and (resid 18 through 318 or resid 323 through 512 or resid 517 throu \ gh 1119)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 15872 2.51 5 N 4112 2.21 5 O 4726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 7.650 Check model and map are aligned: 0.360 Convert atoms to be neutral: 0.170 Process input model: 64.690 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.007 0.080 25433 Z= 0.432 Angle : 1.044 20.239 34613 Z= 0.585 Chirality : 0.060 0.700 3918 Planarity : 0.008 0.073 4485 Dihedral : 9.719 83.092 9030 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.54 % Allowed : 14.34 % Favored : 85.12 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.47 (0.12), residues: 3159 helix: -1.53 (0.17), residues: 635 sheet: -2.07 (0.20), residues: 567 loop : -4.01 (0.11), residues: 1957 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 571 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 577 average time/residue: 0.3865 time to fit residues: 341.8084 Evaluate side-chains 289 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 288 time to evaluate : 2.894 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2268 time to fit residues: 4.2086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 267 optimal weight: 0.9990 chunk 240 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 184 optimal weight: 0.5980 chunk 287 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN A 181 HIS ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN A 699 ASN A 769 GLN A 931 GLN A 935 ASN A 984 GLN A 987 GLN A 993 GLN A1005 ASN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN B 56 GLN B 129 ASN B 181 HIS B 445 HIS B 699 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 ASN B 883 GLN B 937 ASN B1088 GLN C 147 GLN C 181 HIS ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 ASN C 766 GLN C 942 ASN C 947 GLN C 984 GLN C 987 GLN C 993 GLN C1005 ASN ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 25433 Z= 0.220 Angle : 0.720 10.347 34613 Z= 0.380 Chirality : 0.047 0.276 3918 Planarity : 0.006 0.096 4485 Dihedral : 6.877 64.370 3422 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.38 % Favored : 87.31 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.58 (0.13), residues: 3159 helix: -0.01 (0.20), residues: 620 sheet: -1.63 (0.22), residues: 531 loop : -3.64 (0.11), residues: 2008 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 342 time to evaluate : 3.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 33 residues processed: 385 average time/residue: 0.3435 time to fit residues: 213.8783 Evaluate side-chains 278 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 245 time to evaluate : 2.623 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2363 time to fit residues: 18.3762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 159 optimal weight: 8.9990 chunk 89 optimal weight: 0.5980 chunk 239 optimal weight: 0.7980 chunk 196 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 288 optimal weight: 6.9990 chunk 311 optimal weight: 1.9990 chunk 256 optimal weight: 50.0000 chunk 285 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 HIS ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 ASN A 947 GLN A 987 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN B 505 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN B1101 ASN C 304 ASN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 25433 Z= 0.227 Angle : 0.690 9.942 34613 Z= 0.362 Chirality : 0.047 0.208 3918 Planarity : 0.005 0.064 4485 Dihedral : 6.447 64.920 3422 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.82 % Favored : 86.86 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.14), residues: 3159 helix: 0.69 (0.21), residues: 610 sheet: -1.51 (0.22), residues: 549 loop : -3.47 (0.12), residues: 2000 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 270 time to evaluate : 3.073 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: 61 outliers final: 36 residues processed: 318 average time/residue: 0.3454 time to fit residues: 179.4516 Evaluate side-chains 257 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 221 time to evaluate : 2.658 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2195 time to fit residues: 18.9045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 284 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 31 optimal weight: 0.0670 chunk 137 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 289 optimal weight: 9.9990 chunk 306 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 274 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN B 721 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN B1101 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 25433 Z= 0.239 Angle : 0.682 10.039 34613 Z= 0.357 Chirality : 0.046 0.254 3918 Planarity : 0.005 0.060 4485 Dihedral : 6.269 64.042 3422 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.88 % Favored : 86.83 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.14), residues: 3159 helix: 0.94 (0.21), residues: 609 sheet: -1.40 (0.22), residues: 572 loop : -3.38 (0.12), residues: 1978 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 237 time to evaluate : 2.728 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: 45 outliers final: 21 residues processed: 272 average time/residue: 0.3409 time to fit residues: 151.3504 Evaluate side-chains 226 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 205 time to evaluate : 2.802 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2168 time to fit residues: 12.5803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 255 optimal weight: 30.0000 chunk 173 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 228 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 156 optimal weight: 0.8980 chunk 275 optimal weight: 0.0070 chunk 77 optimal weight: 4.9990 overall best weight: 3.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN A 550 GLN A 721 ASN ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 409 ASN B 479 ASN ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN B1101 ASN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.101 25433 Z= 0.410 Angle : 0.786 10.461 34613 Z= 0.411 Chirality : 0.048 0.231 3918 Planarity : 0.005 0.063 4485 Dihedral : 6.566 63.973 3422 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.32 % Allowed : 15.54 % Favored : 84.14 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.14), residues: 3159 helix: 0.69 (0.21), residues: 615 sheet: -1.47 (0.22), residues: 560 loop : -3.41 (0.12), residues: 1984 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 214 time to evaluate : 3.039 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: 49 outliers final: 26 residues processed: 251 average time/residue: 0.3504 time to fit residues: 143.8050 Evaluate side-chains 222 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 2.955 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2587 time to fit residues: 16.0501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 103 optimal weight: 1.9990 chunk 275 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 306 optimal weight: 0.6980 chunk 254 optimal weight: 0.0060 chunk 142 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 GLN A 917 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 409 ASN B 479 ASN B 721 ASN ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.131 25433 Z= 0.203 Angle : 0.676 11.933 34613 Z= 0.353 Chirality : 0.046 0.236 3918 Planarity : 0.004 0.068 4485 Dihedral : 6.139 60.279 3422 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.78 % Favored : 87.94 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.83 (0.14), residues: 3159 helix: 1.03 (0.21), residues: 622 sheet: -1.41 (0.22), residues: 576 loop : -3.25 (0.12), residues: 1961 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 244 time to evaluate : 2.976 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 outliers start: 27 outliers final: 10 residues processed: 267 average time/residue: 0.3666 time to fit residues: 161.0128 Evaluate side-chains 209 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 199 time to evaluate : 2.846 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2234 time to fit residues: 8.1801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 295 optimal weight: 3.9990 chunk 34 optimal weight: 0.0870 chunk 174 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 258 optimal weight: 30.0000 chunk 171 optimal weight: 10.0000 chunk 305 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.106 25433 Z= 0.224 Angle : 0.690 17.254 34613 Z= 0.359 Chirality : 0.047 0.280 3918 Planarity : 0.004 0.075 4485 Dihedral : 6.039 59.764 3422 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.23 % Favored : 86.51 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.14), residues: 3159 helix: 1.05 (0.21), residues: 620 sheet: -1.40 (0.22), residues: 592 loop : -3.19 (0.13), residues: 1947 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 215 time to evaluate : 3.187 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: 27 outliers final: 14 residues processed: 232 average time/residue: 0.3653 time to fit residues: 138.9551 Evaluate side-chains 213 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 199 time to evaluate : 2.843 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2259 time to fit residues: 9.9736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 189 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 182 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 208 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 240 optimal weight: 0.1980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.116 25433 Z= 0.212 Angle : 0.675 13.502 34613 Z= 0.352 Chirality : 0.046 0.251 3918 Planarity : 0.005 0.093 4485 Dihedral : 5.925 59.874 3422 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.12 % Favored : 87.59 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.15), residues: 3159 helix: 1.19 (0.22), residues: 616 sheet: -1.34 (0.22), residues: 592 loop : -3.13 (0.13), residues: 1951 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 226 time to evaluate : 2.900 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 outliers start: 16 outliers final: 7 residues processed: 238 average time/residue: 0.3842 time to fit residues: 151.2959 Evaluate side-chains 211 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 204 time to evaluate : 3.082 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2350 time to fit residues: 7.3353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 277 optimal weight: 4.9990 chunk 292 optimal weight: 6.9990 chunk 267 optimal weight: 0.9990 chunk 284 optimal weight: 0.5980 chunk 171 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 223 optimal weight: 5.9990 chunk 87 optimal weight: 0.1980 chunk 257 optimal weight: 0.9990 chunk 269 optimal weight: 6.9990 chunk 283 optimal weight: 0.5980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.123 25433 Z= 0.186 Angle : 0.666 12.637 34613 Z= 0.347 Chirality : 0.046 0.244 3918 Planarity : 0.005 0.091 4485 Dihedral : 5.721 58.427 3422 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.12 % Favored : 87.62 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.15), residues: 3159 helix: 1.20 (0.22), residues: 615 sheet: -1.28 (0.22), residues: 614 loop : -3.06 (0.13), residues: 1930 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 244 time to evaluate : 2.827 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: 15 outliers final: 6 residues processed: 253 average time/residue: 0.3356 time to fit residues: 140.4140 Evaluate side-chains 217 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 211 time to evaluate : 2.889 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2153 time to fit residues: 6.4661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 186 optimal weight: 4.9990 chunk 301 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 142 optimal weight: 0.5980 chunk 209 optimal weight: 4.9990 chunk 315 optimal weight: 0.7980 chunk 290 optimal weight: 0.7980 chunk 251 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 GLN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.149 25433 Z= 0.220 Angle : 0.698 18.500 34613 Z= 0.361 Chirality : 0.047 0.334 3918 Planarity : 0.005 0.105 4485 Dihedral : 5.742 58.026 3422 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.16 % Favored : 87.59 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.58 (0.15), residues: 3159 helix: 1.14 (0.22), residues: 614 sheet: -1.27 (0.22), residues: 614 loop : -3.04 (0.13), residues: 1931 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 220 time to evaluate : 3.018 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: 7 outliers final: 3 residues processed: 225 average time/residue: 0.3374 time to fit residues: 127.9190 Evaluate side-chains 208 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 205 time to evaluate : 2.980 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2336 time to fit residues: 5.1241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 199 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 251 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 258 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN A 759 ASN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 409 ASN B 479 ASN B 721 ASN ** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.111676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.086292 restraints weight = 88904.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.086607 restraints weight = 60189.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.088108 restraints weight = 42196.965| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.145 25433 Z= 0.355 Angle : 0.766 12.979 34613 Z= 0.399 Chirality : 0.048 0.280 3918 Planarity : 0.005 0.095 4485 Dihedral : 6.107 58.518 3422 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.28 % Allowed : 14.62 % Favored : 85.09 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.15), residues: 3159 helix: 0.88 (0.21), residues: 618 sheet: -1.31 (0.22), residues: 589 loop : -3.11 (0.13), residues: 1952 =============================================================================== Job complete usr+sys time: 4290.58 seconds wall clock time: 79 minutes 46.26 seconds (4786.26 seconds total)