Starting phenix.real_space_refine (version: dev) on Sat Feb 25 07:34:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h10_34420/02_2023/8h10_34420_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h10_34420/02_2023/8h10_34420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h10_34420/02_2023/8h10_34420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h10_34420/02_2023/8h10_34420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h10_34420/02_2023/8h10_34420_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h10_34420/02_2023/8h10_34420_updated.pdb" } resolution = 2.99 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= 0.000 sd= 0.006 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 Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A ASP 518": "OD1" <-> "OD2" Residue "A PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "A ASP 557": "OD1" <-> "OD2" Residue "A TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 296": "OD1" <-> "OD2" Residue "B TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 502": "OE1" <-> "OE2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 554": "OD1" <-> "OD2" Residue "B ASP 557": "OD1" <-> "OD2" Residue "B TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 48": "NH1" <-> "NH2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 296": "OD1" <-> "OD2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "C TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 502": "OE1" <-> "OE2" Residue "C ASP 518": "OD1" <-> "OD2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 554": "OD1" <-> "OD2" Residue "C ASP 557": "OD1" <-> "OD2" Residue "C TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 24882 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8007 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 51, 'TRANS': 974} Chain breaks: 6 Chain: "B" Number of atoms: 8007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8007 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 51, 'TRANS': 974} Chain breaks: 6 Chain: "C" Number of atoms: 8007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8007 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 51, 'TRANS': 974} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 259 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 259 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 259 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 13.40, per 1000 atoms: 0.54 Number of scatterers: 24882 At special positions: 0 Unit cell: (122.64, 127.02, 177.39, 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 4818 8.00 N 4035 7.00 C 15894 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.04 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.04 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1302 " - " ASN A1080 " " NAG A1303 " - " ASN A 109 " " NAG A1304 " - " ASN A 119 " " NAG A1305 " - " ASN A 158 " " NAG A1306 " - " ASN A 269 " " NAG A1307 " - " ASN A 318 " " NAG A1308 " - " ASN A 357 " " NAG A1309 " - " ASN A 602 " " NAG A1310 " - " ASN A 691 " " NAG A1311 " - " ASN A 699 " " NAG A1312 " - " ASN A 783 " " NAG A1313 " - " ASN A1056 " " NAG A1315 " - " ASN A1116 " " NAG B1301 " - " ASN B 65 " " NAG B1302 " - " ASN B1080 " " NAG B1303 " - " ASN B 109 " " NAG B1304 " - " ASN B 119 " " NAG B1305 " - " ASN B 158 " " NAG B1306 " - " ASN B 269 " " NAG B1307 " - " ASN B 318 " " NAG B1308 " - " ASN B 357 " " NAG B1309 " - " ASN B 602 " " NAG B1310 " - " ASN B 691 " " NAG B1311 " - " ASN B 699 " " NAG B1312 " - " ASN B 783 " " NAG B1313 " - " ASN B1056 " " NAG B1315 " - " ASN B1116 " " NAG C1302 " - " ASN C 65 " " NAG C1303 " - " ASN C1080 " " NAG C1304 " - " ASN C 109 " " NAG C1305 " - " ASN C 119 " " NAG C1306 " - " ASN C 158 " " NAG C1307 " - " ASN C 269 " " NAG C1308 " - " ASN C 318 " " NAG C1309 " - " ASN C 357 " " NAG C1310 " - " ASN C 602 " " NAG C1311 " - " ASN C 691 " " NAG C1312 " - " ASN C 699 " " NAG C1313 " - " ASN C 783 " " NAG C1314 " - " ASN C1056 " " NAG C1316 " - " ASN C1116 " " NAG D 1 " - " ASN A 227 " " NAG E 1 " - " ASN B 227 " " NAG F 1 " - " ASN C 227 " Time building additional restraints: 9.92 Conformation dependent library (CDL) restraints added in 3.6 seconds 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5778 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 39 sheets defined 22.9% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.04 Creating SS restraints... Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.670A pdb=" N VAL A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 426 through 429 No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 603 through 610 removed outlier: 3.879A pdb=" N VAL A 606 " --> pdb=" O CYS A 603 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N SER A 607 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 608 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 610 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'A' and resid 617 through 620 No H-bonds generated for 'chain 'A' and resid 617 through 620' Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 729 through 737 removed outlier: 3.934A pdb=" N GLN A 737 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 764 removed outlier: 3.889A pdb=" N ARG A 747 " --> pdb=" O THR A 743 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 748 " --> pdb=" O GLN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 799 through 806 removed outlier: 3.635A pdb=" N ASN A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 838 Processing helix chain 'A' and resid 849 through 865 Processing helix chain 'A' and resid 880 through 891 removed outlier: 3.764A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 900 removed outlier: 3.595A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 921 Processing helix chain 'A' and resid 928 through 949 removed outlier: 4.033A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER A 949 " --> pdb=" O VAL A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 962 No H-bonds generated for 'chain 'A' and resid 959 through 962' Processing helix chain 'A' and resid 968 through 1014 removed outlier: 3.739A pdb=" N VAL A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 391 through 396 removed outlier: 3.669A pdb=" N VAL B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 426 through 429 No H-bonds generated for 'chain 'B' and resid 426 through 429' Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 603 through 610 removed outlier: 3.879A pdb=" N VAL B 606 " --> pdb=" O CYS B 603 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N SER B 607 " --> pdb=" O THR B 604 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 608 " --> pdb=" O ASP B 605 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 610 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 617 through 620 No H-bonds generated for 'chain 'B' and resid 617 through 620' Processing helix chain 'B' and resid 720 through 724 Processing helix chain 'B' and resid 729 through 737 removed outlier: 3.934A pdb=" N GLN B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 764 removed outlier: 3.889A pdb=" N ARG B 747 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 748 " --> pdb=" O GLN B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 787 No H-bonds generated for 'chain 'B' and resid 785 through 787' Processing helix chain 'B' and resid 799 through 806 removed outlier: 3.634A pdb=" N ASN B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 838 Processing helix chain 'B' and resid 849 through 865 Processing helix chain 'B' and resid 880 through 891 removed outlier: 3.764A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 900 removed outlier: 3.595A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 921 Processing helix chain 'B' and resid 928 through 949 removed outlier: 4.032A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER B 949 " --> pdb=" O VAL B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 962 No H-bonds generated for 'chain 'B' and resid 959 through 962' Processing helix chain 'B' and resid 968 through 1014 removed outlier: 3.738A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 325 through 329 Processing helix chain 'C' and resid 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.669A pdb=" N VAL C 394 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 426 through 429 No H-bonds generated for 'chain 'C' and resid 426 through 429' Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 603 through 610 removed outlier: 3.879A pdb=" N VAL C 606 " --> pdb=" O CYS C 603 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N SER C 607 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 608 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 610 " --> pdb=" O SER C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 614 No H-bonds generated for 'chain 'C' and resid 612 through 614' Processing helix chain 'C' and resid 617 through 620 No H-bonds generated for 'chain 'C' and resid 617 through 620' Processing helix chain 'C' and resid 720 through 724 Processing helix chain 'C' and resid 729 through 737 removed outlier: 3.935A pdb=" N GLN C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 764 removed outlier: 3.888A pdb=" N ARG C 747 " --> pdb=" O THR C 743 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 748 " --> pdb=" O GLN C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 787 No H-bonds generated for 'chain 'C' and resid 785 through 787' Processing helix chain 'C' and resid 799 through 806 removed outlier: 3.633A pdb=" N ASN C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 838 Processing helix chain 'C' and resid 849 through 865 Processing helix chain 'C' and resid 880 through 891 removed outlier: 3.764A pdb=" N ILE C 891 " --> pdb=" O ARG C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 900 removed outlier: 3.594A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 921 Processing helix chain 'C' and resid 928 through 949 removed outlier: 4.033A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N SER C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 962 No H-bonds generated for 'chain 'C' and resid 959 through 962' Processing helix chain 'C' and resid 968 through 1014 removed outlier: 3.738A pdb=" N VAL C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.753A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.941A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 230 through 233 removed outlier: 3.977A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 298 through 301 Processing sheet with id= E, first strand: chain 'A' and resid 312 through 315 removed outlier: 6.350A pdb=" N ASN A 526 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ARG A 315 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN A 528 " --> pdb=" O ARG A 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.954A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN A 381 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 502 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 439 through 441 Processing sheet with id= H, first strand: chain 'A' and resid 537 through 540 removed outlier: 5.211A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 673 through 678 removed outlier: 6.541A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 693 through 697 removed outlier: 4.048A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 699 through 710 removed outlier: 3.916A pdb=" N MET A1032 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.519A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1070 through 1072 Processing sheet with id= N, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.753A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.789A 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: 6.317A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.941A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 230 through 233 removed outlier: 3.976A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 298 through 301 Processing sheet with id= R, first strand: chain 'B' and resid 312 through 315 removed outlier: 6.351A pdb=" N ASN B 526 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ARG B 315 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASN B 528 " --> pdb=" O ARG B 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.954A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN B 381 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 502 " --> pdb=" O ASN B 381 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 439 through 441 Processing sheet with id= U, first strand: chain 'B' and resid 537 through 540 removed outlier: 5.211A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 673 through 678 removed outlier: 6.541A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 693 through 697 removed outlier: 4.047A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 699 through 710 removed outlier: 3.916A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.521A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 1070 through 1072 Processing sheet with id= AA, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.754A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 51 through 59 removed outlier: 3.941A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 230 through 233 removed outlier: 3.977A pdb=" N PHE C 161 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 298 through 301 Processing sheet with id= AE, first strand: chain 'C' and resid 312 through 315 removed outlier: 6.351A pdb=" N ASN C 526 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ARG C 315 " --> pdb=" O ASN C 526 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN C 528 " --> pdb=" O ARG C 315 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.955A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 502 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 439 through 441 Processing sheet with id= AH, first strand: chain 'C' and resid 537 through 540 removed outlier: 5.211A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 673 through 678 removed outlier: 6.541A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 693 through 697 removed outlier: 4.048A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 699 through 710 removed outlier: 3.916A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.520A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 1070 through 1072 849 hydrogen bonds defined for protein. 2340 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: 10.02 Time building geometry restraints manager: 10.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4011 1.31 - 1.44: 7158 1.44 - 1.58: 14097 1.58 - 1.71: 0 1.71 - 1.84: 180 Bond restraints: 25446 Sorted by residual: bond pdb=" C1C BLA B1314 " pdb=" NC BLA B1314 " ideal model delta sigma weight residual 1.368 1.534 -0.166 2.00e-02 2.50e+03 6.88e+01 bond pdb=" C1C BLA C1315 " pdb=" NC BLA C1315 " ideal model delta sigma weight residual 1.368 1.534 -0.166 2.00e-02 2.50e+03 6.85e+01 bond pdb=" C1C BLA A1314 " pdb=" NC BLA A1314 " ideal model delta sigma weight residual 1.368 1.533 -0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" C4C BLA B1314 " pdb=" NC BLA B1314 " ideal model delta sigma weight residual 1.375 1.538 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" C4C BLA C1315 " pdb=" NC BLA C1315 " ideal model delta sigma weight residual 1.375 1.538 -0.163 2.00e-02 2.50e+03 6.61e+01 ... (remaining 25441 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.94: 581 105.94 - 112.96: 13570 112.96 - 119.99: 8491 119.99 - 127.02: 11741 127.02 - 134.04: 228 Bond angle restraints: 34611 Sorted by residual: angle pdb=" N ASN A 589 " pdb=" CA ASN A 589 " pdb=" C ASN A 589 " ideal model delta sigma weight residual 114.64 106.26 8.38 1.52e+00 4.33e-01 3.04e+01 angle pdb=" N ASN C 589 " pdb=" CA ASN C 589 " pdb=" C ASN C 589 " ideal model delta sigma weight residual 114.64 106.27 8.37 1.52e+00 4.33e-01 3.03e+01 angle pdb=" N ASN B 589 " pdb=" CA ASN B 589 " pdb=" C ASN B 589 " ideal model delta sigma weight residual 114.64 106.31 8.33 1.52e+00 4.33e-01 3.00e+01 angle pdb=" CA GLN C1124 " pdb=" CB GLN C1124 " pdb=" CG GLN C1124 " ideal model delta sigma weight residual 114.10 123.72 -9.62 2.00e+00 2.50e-01 2.31e+01 angle pdb=" CA GLN A1124 " pdb=" CB GLN A1124 " pdb=" CG GLN A1124 " ideal model delta sigma weight residual 114.10 123.69 -9.59 2.00e+00 2.50e-01 2.30e+01 ... (remaining 34606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 13448 15.24 - 30.47: 1186 30.47 - 45.71: 288 45.71 - 60.94: 63 60.94 - 76.18: 36 Dihedral angle restraints: 15021 sinusoidal: 6045 harmonic: 8976 Sorted by residual: dihedral pdb=" CB CYS B 467 " pdb=" SG CYS B 467 " pdb=" SG CYS B 474 " pdb=" CB CYS B 474 " ideal model delta sinusoidal sigma weight residual -86.00 -154.63 68.63 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CB CYS A 467 " pdb=" SG CYS A 467 " pdb=" SG CYS A 474 " pdb=" CB CYS A 474 " ideal model delta sinusoidal sigma weight residual -86.00 -154.61 68.61 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CB CYS C 467 " pdb=" SG CYS C 467 " pdb=" SG CYS C 474 " pdb=" CB CYS C 474 " ideal model delta sinusoidal sigma weight residual -86.00 -154.60 68.60 1 1.00e+01 1.00e-02 6.10e+01 ... (remaining 15018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3484 0.077 - 0.153: 501 0.153 - 0.230: 44 0.230 - 0.306: 0 0.306 - 0.383: 3 Chirality restraints: 4032 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.77e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 65 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 65 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 4029 not shown) Planarity restraints: 4449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA C1315 " -0.221 2.00e-02 2.50e+03 2.63e-01 1.72e+03 pdb=" C1A BLA C1315 " 0.613 2.00e-02 2.50e+03 pdb=" C1D BLA C1315 " -0.045 2.00e-02 2.50e+03 pdb=" C2D BLA C1315 " 0.058 2.00e-02 2.50e+03 pdb=" C3D BLA C1315 " -0.061 2.00e-02 2.50e+03 pdb=" C4D BLA C1315 " -0.244 2.00e-02 2.50e+03 pdb=" CAD BLA C1315 " -0.011 2.00e-02 2.50e+03 pdb=" CHA BLA C1315 " -0.369 2.00e-02 2.50e+03 pdb=" CHD BLA C1315 " 0.036 2.00e-02 2.50e+03 pdb=" CMD BLA C1315 " 0.243 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA B1314 " -0.221 2.00e-02 2.50e+03 2.62e-01 1.72e+03 pdb=" C1A BLA B1314 " 0.612 2.00e-02 2.50e+03 pdb=" C1D BLA B1314 " -0.045 2.00e-02 2.50e+03 pdb=" C2D BLA B1314 " 0.057 2.00e-02 2.50e+03 pdb=" C3D BLA B1314 " -0.060 2.00e-02 2.50e+03 pdb=" C4D BLA B1314 " -0.243 2.00e-02 2.50e+03 pdb=" CAD BLA B1314 " -0.010 2.00e-02 2.50e+03 pdb=" CHA BLA B1314 " -0.370 2.00e-02 2.50e+03 pdb=" CHD BLA B1314 " 0.037 2.00e-02 2.50e+03 pdb=" CMD BLA B1314 " 0.243 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA A1314 " -0.221 2.00e-02 2.50e+03 2.62e-01 1.72e+03 pdb=" C1A BLA A1314 " 0.612 2.00e-02 2.50e+03 pdb=" C1D BLA A1314 " -0.045 2.00e-02 2.50e+03 pdb=" C2D BLA A1314 " 0.058 2.00e-02 2.50e+03 pdb=" C3D BLA A1314 " -0.061 2.00e-02 2.50e+03 pdb=" C4D BLA A1314 " -0.243 2.00e-02 2.50e+03 pdb=" CAD BLA A1314 " -0.011 2.00e-02 2.50e+03 pdb=" CHA BLA A1314 " -0.369 2.00e-02 2.50e+03 pdb=" CHD BLA A1314 " 0.037 2.00e-02 2.50e+03 pdb=" CMD BLA A1314 " 0.243 2.00e-02 2.50e+03 ... (remaining 4446 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7553 2.82 - 3.34: 20089 3.34 - 3.86: 38546 3.86 - 4.38: 44806 4.38 - 4.90: 79842 Nonbonded interactions: 190836 Sorted by model distance: nonbonded pdb=" OH TYR C 436 " pdb=" OH TYR C 484 " model vdw 2.304 2.440 nonbonded pdb=" OH TYR A 436 " pdb=" OH TYR A 484 " model vdw 2.305 2.440 nonbonded pdb=" OH TYR B 436 " pdb=" OH TYR B 484 " model vdw 2.305 2.440 nonbonded pdb=" NH1 ARG A1073 " pdb=" O ASP A1100 " model vdw 2.325 2.520 nonbonded pdb=" NH1 ARG B1073 " pdb=" O ASP B1100 " model vdw 2.326 2.520 ... (remaining 190831 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 31 through 1125 or resid 1302 through 1313)) selection = (chain 'B' and (resid 31 through 1125 or resid 1302 through 1313)) selection = (chain 'C' and (resid 31 through 1125 or resid 1302 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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 15894 2.51 5 N 4035 2.21 5 O 4818 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.490 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: 0.020 Extract box with map and model: 9.530 Check model and map are aligned: 0.350 Process input model: 62.740 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.008 0.166 25446 Z= 0.516 Angle : 0.875 11.693 34611 Z= 0.472 Chirality : 0.054 0.383 4032 Planarity : 0.010 0.263 4404 Dihedral : 12.771 76.178 9126 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3036 helix: -0.06 (0.20), residues: 684 sheet: 0.91 (0.20), residues: 717 loop : -1.84 (0.13), residues: 1635 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 273 time to evaluate : 2.822 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 0 residues processed: 279 average time/residue: 1.3918 time to fit residues: 451.6626 Evaluate side-chains 160 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.956 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.9990 chunk 231 optimal weight: 0.2980 chunk 128 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 239 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 277 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 632 GLN A 769 GLN A 883 GLN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 GLN B 632 GLN B 769 GLN B 889 ASN B1065 HIS C 155 ASN C 523 GLN C 632 GLN C 769 GLN C 883 GLN ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 25446 Z= 0.172 Angle : 0.538 7.915 34611 Z= 0.284 Chirality : 0.044 0.336 4032 Planarity : 0.005 0.108 4404 Dihedral : 6.249 86.951 3666 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 3036 helix: 0.82 (0.21), residues: 666 sheet: 0.90 (0.20), residues: 726 loop : -1.60 (0.14), residues: 1644 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 166 time to evaluate : 3.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 9 residues processed: 182 average time/residue: 1.0583 time to fit residues: 235.7551 Evaluate side-chains 155 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 2.964 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.2876 time to fit residues: 5.3680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 189 optimal weight: 0.0980 chunk 76 optimal weight: 0.0970 chunk 278 optimal weight: 2.9990 chunk 300 optimal weight: 0.7980 chunk 247 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 ASN A 889 ASN B 746 ASN C 733 ASN C 746 ASN C 889 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 25446 Z= 0.232 Angle : 0.536 7.347 34611 Z= 0.285 Chirality : 0.045 0.319 4032 Planarity : 0.005 0.103 4404 Dihedral : 6.052 89.646 3666 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 3036 helix: 1.20 (0.21), residues: 660 sheet: 0.80 (0.20), residues: 738 loop : -1.58 (0.14), residues: 1638 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 160 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 20 residues processed: 186 average time/residue: 1.0509 time to fit residues: 238.1747 Evaluate side-chains 171 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 2.754 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.3905 time to fit residues: 7.6104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 0.0030 chunk 209 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 264 optimal weight: 0.0570 chunk 79 optimal weight: 1.9990 overall best weight: 1.0114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 733 ASN C 112 GLN C 733 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 25446 Z= 0.197 Angle : 0.505 6.758 34611 Z= 0.269 Chirality : 0.044 0.319 4032 Planarity : 0.004 0.098 4404 Dihedral : 5.860 88.123 3666 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3036 helix: 1.47 (0.22), residues: 654 sheet: 0.78 (0.20), residues: 741 loop : -1.45 (0.14), residues: 1641 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 156 time to evaluate : 2.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 33 residues processed: 192 average time/residue: 1.0123 time to fit residues: 240.3240 Evaluate side-chains 175 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 2.859 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 25 residues processed: 8 average time/residue: 0.3634 time to fit residues: 8.5318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 252 optimal weight: 0.8980 chunk 204 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 0.3980 chunk 265 optimal weight: 0.9980 chunk 74 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 733 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 25446 Z= 0.150 Angle : 0.478 8.182 34611 Z= 0.256 Chirality : 0.043 0.318 4032 Planarity : 0.004 0.091 4404 Dihedral : 5.649 88.806 3666 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3036 helix: 1.69 (0.22), residues: 651 sheet: 0.80 (0.20), residues: 747 loop : -1.35 (0.14), residues: 1638 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 156 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 31 residues processed: 201 average time/residue: 1.0341 time to fit residues: 255.6564 Evaluate side-chains 175 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 2.895 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 27 residues processed: 4 average time/residue: 0.3978 time to fit residues: 6.6279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 0.6980 chunk 266 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 173 optimal weight: 0.2980 chunk 73 optimal weight: 0.8980 chunk 296 optimal weight: 0.9980 chunk 245 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 546 GLN B 733 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 25446 Z= 0.158 Angle : 0.479 6.237 34611 Z= 0.257 Chirality : 0.043 0.315 4032 Planarity : 0.004 0.088 4404 Dihedral : 5.548 88.309 3666 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 3036 helix: 1.79 (0.22), residues: 651 sheet: 0.81 (0.19), residues: 747 loop : -1.31 (0.14), residues: 1638 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 150 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 36 residues processed: 192 average time/residue: 1.0773 time to fit residues: 252.8274 Evaluate side-chains 181 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 2.858 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 29 residues processed: 7 average time/residue: 0.5621 time to fit residues: 9.4733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 GLN B 546 GLN B 549 GLN B 733 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 25446 Z= 0.310 Angle : 0.550 8.002 34611 Z= 0.295 Chirality : 0.046 0.318 4032 Planarity : 0.005 0.087 4404 Dihedral : 5.740 89.854 3666 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3036 helix: 1.44 (0.21), residues: 666 sheet: 0.81 (0.20), residues: 735 loop : -1.45 (0.14), residues: 1635 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 151 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 39 residues processed: 194 average time/residue: 1.0081 time to fit residues: 242.7421 Evaluate side-chains 182 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 143 time to evaluate : 2.829 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 30 residues processed: 9 average time/residue: 0.3290 time to fit residues: 8.5485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 1.9990 chunk 117 optimal weight: 0.0070 chunk 176 optimal weight: 0.0000 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 231 optimal weight: 0.0470 chunk 268 optimal weight: 2.9990 overall best weight: 0.2900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 883 GLN B 546 GLN B 549 GLN B 733 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 25446 Z= 0.123 Angle : 0.466 6.930 34611 Z= 0.250 Chirality : 0.042 0.302 4032 Planarity : 0.004 0.089 4404 Dihedral : 5.390 86.045 3666 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3036 helix: 1.86 (0.21), residues: 651 sheet: 0.81 (0.19), residues: 753 loop : -1.31 (0.14), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 152 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 32 residues processed: 191 average time/residue: 1.0434 time to fit residues: 245.8615 Evaluate side-chains 169 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 2.859 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 29 residues processed: 3 average time/residue: 0.3655 time to fit residues: 5.6846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 1.9990 chunk 257 optimal weight: 0.0070 chunk 274 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 215 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 259 optimal weight: 0.8980 chunk 273 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN B 546 GLN B 549 GLN B 733 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.070 25446 Z= 0.161 Angle : 0.495 9.855 34611 Z= 0.263 Chirality : 0.043 0.308 4032 Planarity : 0.004 0.089 4404 Dihedral : 5.385 83.285 3666 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3036 helix: 1.93 (0.22), residues: 651 sheet: 0.81 (0.19), residues: 747 loop : -1.25 (0.14), residues: 1638 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 140 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 35 residues processed: 174 average time/residue: 1.0420 time to fit residues: 223.1669 Evaluate side-chains 174 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 2.533 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 30 residues processed: 5 average time/residue: 0.3457 time to fit residues: 6.2344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.0170 chunk 177 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 304 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 242 optimal weight: 0.0980 chunk 25 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.0224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 546 GLN B 549 GLN B 733 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 25446 Z= 0.204 Angle : 0.513 8.053 34611 Z= 0.274 Chirality : 0.044 0.304 4032 Planarity : 0.004 0.091 4404 Dihedral : 5.407 76.446 3666 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 3036 helix: 1.76 (0.21), residues: 663 sheet: 0.81 (0.19), residues: 747 loop : -1.31 (0.14), residues: 1626 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 140 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 35 residues processed: 176 average time/residue: 1.0545 time to fit residues: 229.3451 Evaluate side-chains 172 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 137 time to evaluate : 2.935 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 32 residues processed: 3 average time/residue: 0.3740 time to fit residues: 5.9123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.0870 chunk 74 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 243 optimal weight: 0.0370 chunk 101 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 213 optimal weight: 6.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 GLN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.133962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.100664 restraints weight = 36028.108| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.60 r_work: 0.3068 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 25446 Z= 0.145 Angle : 0.484 8.514 34611 Z= 0.259 Chirality : 0.043 0.297 4032 Planarity : 0.004 0.091 4404 Dihedral : 5.236 69.134 3666 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3036 helix: 1.97 (0.22), residues: 651 sheet: 0.85 (0.20), residues: 744 loop : -1.22 (0.14), residues: 1641 =============================================================================== Job complete usr+sys time: 5846.79 seconds wall clock time: 107 minutes 17.88 seconds (6437.88 seconds total)