Starting phenix.real_space_refine on Sun Nov 19 01:03:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/11_2023/6acd_9589.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/11_2023/6acd_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_9589/11_2023/6acd_9589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/11_2023/6acd_9589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/11_2023/6acd_9589.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6acd_9589/11_2023/6acd_9589.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} 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: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1013} 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: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1006} Chain breaks: 5 Time building chain proxies: 12.81, 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: 9.46 Conformation dependent library (CDL) restraints added in 4.9 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: 2.75 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: 10.52 Time building geometry restraints manager: 10.31 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 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: 1.600 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: 0.030 Extract box with map and model: 6.390 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 66.890 Find NCS groups from input model: 1.590 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: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 : 7.98 Ramachandran Plot: Outliers : 0.54 % Allowed : 14.34 % Favored : 85.12 % Rotamer: Outliers : 0.25 % Allowed : 2.14 % Favored : 97.61 % 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 : 2.615 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: 0.4197 time to fit residues: 364.9866 Evaluate side-chains 289 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 288 time to evaluate : 2.984 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2184 time to fit residues: 4.4067 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25433 Z= 0.214 Angle : 0.714 10.282 34613 Z= 0.376 Chirality : 0.047 0.288 3918 Planarity : 0.005 0.059 4485 Dihedral : 6.836 64.114 3422 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.31 % Favored : 87.37 % Rotamer: Outliers : 2.43 % Allowed : 9.14 % Favored : 88.43 % 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: -3.56 (0.13), residues: 3159 helix: 0.03 (0.20), residues: 620 sheet: -1.62 (0.22), residues: 531 loop : -3.63 (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 411 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 344 time to evaluate : 2.758 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: 67 outliers final: 33 residues processed: 390 average time/residue: 0.3614 time to fit residues: 225.2167 Evaluate side-chains 280 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 247 time to evaluate : 2.742 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2214 time to fit residues: 17.7089 ------------------------------------------------------------------------------- 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: 0.3980 chunk 89 optimal weight: 2.9990 chunk 239 optimal weight: 0.1980 chunk 196 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 288 optimal weight: 1.9990 chunk 311 optimal weight: 0.5980 chunk 256 optimal weight: 40.0000 chunk 285 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 987 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 381 ASN B 505 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN ** B1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 25433 Z= 0.184 Angle : 0.675 9.863 34613 Z= 0.353 Chirality : 0.047 0.212 3918 Planarity : 0.005 0.060 4485 Dihedral : 6.333 63.965 3422 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.55 % Favored : 88.13 % Rotamer: Outliers : 1.99 % Allowed : 9.93 % Favored : 88.07 % 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: -3.10 (0.14), residues: 3159 helix: 0.75 (0.21), residues: 605 sheet: -1.44 (0.22), residues: 551 loop : -3.40 (0.12), residues: 2003 *********************** 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 363 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 308 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 29 residues processed: 351 average time/residue: 0.3559 time to fit residues: 201.2209 Evaluate side-chains 273 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 244 time to evaluate : 2.615 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2385 time to fit residues: 16.7312 ------------------------------------------------------------------------------- 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: 6.9990 chunk 149 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 289 optimal weight: 10.0000 chunk 306 optimal weight: 7.9990 chunk 151 optimal weight: 9.9990 chunk 274 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 523 GLN ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 GLN ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 GLN ** A1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 149 HIS B 280 GLN B 409 ASN ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN B1005 ASN B1101 ASN C 96 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 ASN C 917 GLN ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 25433 Z= 0.544 Angle : 0.917 13.943 34613 Z= 0.480 Chirality : 0.052 0.283 3918 Planarity : 0.006 0.072 4485 Dihedral : 7.096 67.859 3422 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 24.99 Ramachandran Plot: Outliers : 0.44 % Allowed : 16.46 % Favored : 83.10 % Rotamer: Outliers : 3.37 % Allowed : 12.07 % Favored : 84.55 % 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: -3.54 (0.14), residues: 3159 helix: -0.02 (0.19), residues: 632 sheet: -1.82 (0.21), residues: 581 loop : -3.57 (0.12), residues: 1946 *********************** 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 313 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 220 time to evaluate : 3.014 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: 93 outliers final: 58 residues processed: 287 average time/residue: 0.3411 time to fit residues: 160.1769 Evaluate side-chains 251 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 193 time to evaluate : 2.836 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.2413 time to fit residues: 29.6285 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 2.9990 chunk 228 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 211 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 156 optimal weight: 0.9980 chunk 275 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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** ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 721 ASN ** B 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 987 GLN ** 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: 0.7871 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25433 Z= 0.264 Angle : 0.708 11.309 34613 Z= 0.371 Chirality : 0.047 0.295 3918 Planarity : 0.005 0.069 4485 Dihedral : 6.491 63.229 3422 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.66 % Favored : 87.02 % Rotamer: Outliers : 1.05 % Allowed : 13.34 % Favored : 85.61 % 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: -3.07 (0.14), residues: 3159 helix: 0.81 (0.21), residues: 615 sheet: -1.47 (0.22), residues: 558 loop : -3.40 (0.12), residues: 1986 *********************** 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: 29 poor density : 234 time to evaluate : 2.785 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: 29 outliers final: 16 residues processed: 254 average time/residue: 0.3699 time to fit residues: 152.3240 Evaluate side-chains 216 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 200 time to evaluate : 2.523 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2291 time to fit residues: 10.6442 ------------------------------------------------------------------------------- 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: 0.7980 chunk 275 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 306 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 744 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 939 GLN ** 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25433 Z= 0.304 Angle : 0.724 11.188 34613 Z= 0.378 Chirality : 0.047 0.233 3918 Planarity : 0.005 0.060 4485 Dihedral : 6.409 61.011 3422 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.28 % Allowed : 14.91 % Favored : 84.81 % Rotamer: Outliers : 1.78 % Allowed : 13.74 % Favored : 84.48 % 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: -3.05 (0.14), residues: 3159 helix: 0.79 (0.21), residues: 617 sheet: -1.48 (0.22), residues: 563 loop : -3.37 (0.12), residues: 1979 *********************** 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 269 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 220 time to evaluate : 2.720 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 outliers start: 49 outliers final: 21 residues processed: 261 average time/residue: 0.3592 time to fit residues: 153.8059 Evaluate side-chains 221 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 200 time to evaluate : 2.812 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2501 time to fit residues: 13.5318 ------------------------------------------------------------------------------- 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: 1.9990 chunk 34 optimal weight: 0.3980 chunk 174 optimal weight: 3.9990 chunk 223 optimal weight: 20.0000 chunk 173 optimal weight: 0.6980 chunk 258 optimal weight: 30.0000 chunk 171 optimal weight: 9.9990 chunk 305 optimal weight: 0.4980 chunk 191 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 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 721 ASN ** B 895 GLN ** 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 744 GLN ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 25433 Z= 0.203 Angle : 0.685 13.318 34613 Z= 0.357 Chirality : 0.047 0.272 3918 Planarity : 0.004 0.057 4485 Dihedral : 6.171 60.074 3422 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.03 % Favored : 87.69 % Rotamer: Outliers : 0.83 % Allowed : 14.39 % Favored : 84.77 % 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: -2.85 (0.14), residues: 3159 helix: 1.04 (0.22), residues: 612 sheet: -1.41 (0.22), residues: 588 loop : -3.26 (0.12), residues: 1959 *********************** 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 265 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 242 time to evaluate : 2.908 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: 23 outliers final: 7 residues processed: 259 average time/residue: 0.3389 time to fit residues: 145.3190 Evaluate side-chains 215 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 208 time to evaluate : 2.786 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2329 time to fit residues: 6.7547 ------------------------------------------------------------------------------- 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: 2.9990 chunk 122 optimal weight: 10.0000 chunk 182 optimal weight: 0.0370 chunk 92 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- 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 632 GLN ** A 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN B 993 GLN 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** ** C1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 25433 Z= 0.314 Angle : 0.736 14.447 34613 Z= 0.382 Chirality : 0.047 0.314 3918 Planarity : 0.005 0.059 4485 Dihedral : 6.252 59.944 3422 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.32 % Allowed : 14.59 % Favored : 85.09 % Rotamer: Outliers : 0.83 % Allowed : 15.26 % Favored : 83.90 % 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: -2.93 (0.14), residues: 3159 helix: 0.92 (0.22), residues: 607 sheet: -1.45 (0.22), residues: 589 loop : -3.28 (0.12), residues: 1963 *********************** 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 231 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 208 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 223 average time/residue: 0.3643 time to fit residues: 132.9594 Evaluate side-chains 208 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 195 time to evaluate : 2.981 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2900 time to fit residues: 10.5455 ------------------------------------------------------------------------------- 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: 0.9990 chunk 171 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 223 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 257 optimal weight: 20.0000 chunk 269 optimal weight: 2.9990 chunk 283 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 632 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 721 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN 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** C1005 ASN ** C1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25433 Z= 0.271 Angle : 0.718 13.515 34613 Z= 0.374 Chirality : 0.047 0.268 3918 Planarity : 0.004 0.058 4485 Dihedral : 6.200 59.582 3422 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.61 % Favored : 86.10 % Rotamer: Outliers : 0.58 % Allowed : 15.55 % Favored : 83.87 % 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: -2.86 (0.15), residues: 3159 helix: 0.99 (0.22), residues: 614 sheet: -1.44 (0.22), residues: 591 loop : -3.24 (0.12), residues: 1954 *********************** 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 222 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 217 average time/residue: 0.3449 time to fit residues: 123.1470 Evaluate side-chains 208 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 200 time to evaluate : 2.735 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2241 time to fit residues: 7.1722 ------------------------------------------------------------------------------- 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: 0.9990 chunk 301 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 209 optimal weight: 0.9990 chunk 315 optimal weight: 0.0970 chunk 290 optimal weight: 0.0000 chunk 251 optimal weight: 30.0000 chunk 26 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 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 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: 0.7803 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25433 Z= 0.178 Angle : 0.691 14.629 34613 Z= 0.356 Chirality : 0.047 0.290 3918 Planarity : 0.004 0.058 4485 Dihedral : 5.910 58.404 3422 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.41 % Favored : 87.34 % Rotamer: Outliers : 0.33 % Allowed : 15.77 % Favored : 83.90 % 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: -2.68 (0.15), residues: 3159 helix: 1.16 (0.22), residues: 615 sheet: -1.34 (0.22), residues: 608 loop : -3.14 (0.13), residues: 1936 ********************** 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 256 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 247 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 251 average time/residue: 0.3497 time to fit residues: 144.6347 Evaluate side-chains 212 residues out of total 2758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 209 time to evaluate : 2.697 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2263 time to fit residues: 5.0809 ------------------------------------------------------------------------------- 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: 1.9990 chunk 267 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 251 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 31 optimal weight: 0.0670 chunk 46 optimal weight: 5.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- 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 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 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 135 ASN B 721 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 ASN ** 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 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN ** C1107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.115485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.089816 restraints weight = 88321.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.090244 restraints weight = 53210.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.091318 restraints weight = 39305.525| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25433 Z= 0.210 Angle : 0.699 17.259 34613 Z= 0.361 Chirality : 0.047 0.330 3918 Planarity : 0.004 0.057 4485 Dihedral : 5.881 58.012 3422 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.76 % Favored : 86.99 % Rotamer: Outliers : 0.47 % Allowed : 15.74 % Favored : 83.79 % 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: -2.62 (0.15), residues: 3159 helix: 1.21 (0.22), residues: 609 sheet: -1.30 (0.22), residues: 619 loop : -3.09 (0.13), residues: 1931 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4532.11 seconds wall clock time: 84 minutes 17.88 seconds (5057.88 seconds total)