Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 12 12:04:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0y_34418/10_2023/8h0y_34418_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0y_34418/10_2023/8h0y_34418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0y_34418/10_2023/8h0y_34418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0y_34418/10_2023/8h0y_34418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0y_34418/10_2023/8h0y_34418_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h0y_34418/10_2023/8h0y_34418_updated.pdb" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 15977 2.51 5 N 4056 2.21 5 O 4825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B ASP 376": "OD1" <-> "OD2" Residue "B PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 502": "OE1" <-> "OE2" Residue "B ASP 572": "OD1" <-> "OD2" Residue "B TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 762": "OE1" <-> "OE2" Residue "B TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 830": "OD1" <-> "OD2" Residue "B TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 999": "OE1" <-> "OE2" Residue "B PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 600": "OD1" <-> "OD2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 821": "OE1" <-> "OE2" Residue "A ASP 976": "OD1" <-> "OD2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 204": "OD1" <-> "OD2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 415": "OD1" <-> "OD2" Residue "C PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 649": "OD1" <-> "OD2" Residue "C ASP 684": "OD1" <-> "OD2" Residue "C ASP 727": "OD1" <-> "OD2" Residue "C TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 755": "OE1" <-> "OE2" Residue "C PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 821": "OE1" <-> "OE2" Residue "C ASP 830": "OD1" <-> "OD2" Residue "C GLU 970": "OE1" <-> "OE2" Residue "C GLU 1054": "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-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 24999 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7974 Classifications: {'peptide': 1019} Link IDs: {'PTRANS': 49, 'TRANS': 969} Chain breaks: 9 Chain: "A" Number of atoms: 8143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8143 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 50, 'TRANS': 993} Chain breaks: 6 Chain: "C" Number of atoms: 8049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8049 Classifications: {'peptide': 1031} Link IDs: {'PTRANS': 49, 'TRANS': 981} Chain breaks: 6 Chain: "B" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 287 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 16} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen chiralities: 16 Chain: "A" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 273 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 15} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 273 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 15} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 12.61, per 1000 atoms: 0.50 Number of scatterers: 24999 At special positions: 0 Unit cell: (121.545, 125.925, 174.105, 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 141 16.00 O 4825 8.00 N 4056 7.00 C 15977 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.05 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 370 " - pdb=" SG CYS C 967 " distance=2.05 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS A 370 " 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 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=2.05 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.04 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS C 370 " distance=2.05 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 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=2.05 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.07 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 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 NAG-ASN " NAG A1302 " - " ASN A1056 " " NAG A1303 " - " ASN A 65 " " NAG A1304 " - " ASN A1080 " " NAG A1305 " - " ASN A 109 " " NAG A1306 " - " ASN A 119 " " NAG A1307 " - " ASN A 158 " " NAG A1308 " - " ASN A 227 " " NAG A1309 " - " ASN A 269 " " NAG A1310 " - " ASN A 318 " " NAG A1311 " - " ASN A 330 " " NAG A1312 " - " ASN A 357 " " NAG A1313 " - " ASN A 602 " " NAG A1314 " - " ASN A 699 " " NAG A1315 " - " ASN A 783 " " NAG A1316 " - " ASN A1116 " " NAG B1302 " - " ASN B1056 " " NAG B1303 " - " ASN B 65 " " NAG B1304 " - " ASN B1080 " " NAG B1305 " - " ASN B 109 " " NAG B1306 " - " ASN B 119 " " NAG B1307 " - " ASN B 158 " " NAG B1308 " - " ASN B 227 " " NAG B1309 " - " ASN B 269 " " NAG B1310 " - " ASN B 318 " " NAG B1311 " - " ASN B 330 " " NAG B1312 " - " ASN B 357 " " NAG B1313 " - " ASN B 602 " " NAG B1314 " - " ASN B 691 " " NAG B1315 " - " ASN B 699 " " NAG B1316 " - " ASN B 783 " " NAG B1317 " - " ASN B1116 " " NAG C1302 " - " ASN C1056 " " NAG C1303 " - " ASN C 65 " " NAG C1304 " - " ASN C1080 " " NAG C1305 " - " ASN C 109 " " NAG C1306 " - " ASN C 119 " " NAG C1307 " - " ASN C 158 " " NAG C1308 " - " ASN C 227 " " NAG C1309 " - " ASN C 269 " " NAG C1310 " - " ASN C 318 " " NAG C1311 " - " ASN C 357 " " NAG C1312 " - " ASN C 602 " " NAG C1313 " - " ASN C 691 " " NAG C1314 " - " ASN C 699 " " NAG C1315 " - " ASN C 783 " " NAG C1316 " - " ASN C1116 " Time building additional restraints: 9.20 Conformation dependent library (CDL) restraints added in 3.2 seconds 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5796 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 37 sheets defined 22.3% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.72 Creating SS restraints... Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 325 through 328 No H-bonds generated for 'chain 'B' and resid 325 through 328' Processing helix chain 'B' and resid 353 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: 3.702A pdb=" N VAL B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 4.278A 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 720 through 724 Processing helix chain 'B' and resid 729 through 736 removed outlier: 3.804A pdb=" N LEU B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 764 removed outlier: 3.769A pdb=" N GLN B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU B 745 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 831 through 838 removed outlier: 3.604A pdb=" N ASN B 838 " --> pdb=" O ALA B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 866 Processing helix chain 'B' and resid 880 through 889 Processing helix chain 'B' and resid 896 through 921 removed outlier: 3.556A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS B 903 " --> pdb=" O TYR B 899 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN B 904 " --> pdb=" O GLU B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 948 removed outlier: 4.038A pdb=" N LEU B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 964 Processing helix chain 'B' and resid 968 through 1014 removed outlier: 3.621A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 325 through 328 No H-bonds generated for 'chain 'A' and resid 325 through 328' Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.752A pdb=" N LEU A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' 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 607 through 610 No H-bonds generated for 'chain 'A' and resid 607 through 610' 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 622 removed outlier: 4.412A pdb=" N TYR A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'A' and resid 729 through 736 removed outlier: 3.803A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 764 removed outlier: 3.868A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A 745 " --> pdb=" O PHE A 741 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (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 807 Processing helix chain 'A' and resid 819 through 823 Processing helix chain 'A' and resid 831 through 838 removed outlier: 3.726A pdb=" N ASN A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 866 Processing helix chain 'A' and resid 869 through 872 No H-bonds generated for 'chain 'A' and resid 869 through 872' Processing helix chain 'A' and resid 880 through 889 Processing helix chain 'A' and resid 895 through 900 removed outlier: 3.759A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 922 removed outlier: 3.758A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 949 removed outlier: 3.922A pdb=" N LEU A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER A 949 " --> pdb=" O VAL A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 965 removed outlier: 3.775A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1014 removed outlier: 3.896A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 325 through 328 No H-bonds generated for 'chain 'C' and resid 325 through 328' 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: 3.618A pdb=" N VAL C 394 " --> pdb=" O GLY C 391 " (cutoff:3.500A) 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 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 720 through 724 Processing helix chain 'C' and resid 729 through 738 removed outlier: 3.686A pdb=" N LEU C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLN C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TYR C 738 " --> pdb=" O LEU C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 764 removed outlier: 3.771A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (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 805 Processing helix chain 'C' and resid 819 through 823 Processing helix chain 'C' and resid 831 through 838 removed outlier: 3.697A pdb=" N ASN C 838 " --> pdb=" O ALA C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 865 Processing helix chain 'C' and resid 880 through 891 removed outlier: 3.556A pdb=" N ILE C 891 " --> pdb=" O ARG C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 899 Processing helix chain 'C' and resid 902 through 921 Processing helix chain 'C' and resid 928 through 949 removed outlier: 3.985A pdb=" N LEU C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N SER C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 963 Processing helix chain 'C' and resid 968 through 1014 removed outlier: 3.600A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.810A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 93 " --> pdb=" O HIS B 181 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 203 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.912A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 161 through 164 removed outlier: 6.643A pdb=" N ILE B 234 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TRP B 101 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG B 232 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE B 103 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASN B 230 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 298 through 302 removed outlier: 4.642A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 312 through 315 removed outlier: 8.547A pdb=" N VAL B 313 " --> pdb=" O CYS B 524 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN B 526 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ARG B 315 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN B 528 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 341 through 345 removed outlier: 4.162A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 439 through 441 Processing sheet with id= H, first strand: chain 'B' and resid 673 through 678 removed outlier: 6.568A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 693 through 697 removed outlier: 3.762A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 699 through 710 removed outlier: 6.184A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.443A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 1063 through 1065 Processing sheet with id= M, first strand: chain 'A' and resid 32 through 35 removed outlier: 4.008A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 93 " --> pdb=" O HIS A 181 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A 181 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 52 through 59 removed outlier: 3.963A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 161 through 164 removed outlier: 6.351A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 298 through 301 Processing sheet with id= Q, first strand: chain 'A' and resid 312 through 315 removed outlier: 8.772A pdb=" N VAL A 313 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASN A 526 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ARG A 315 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASN A 528 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 341 through 345 removed outlier: 4.232A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 439 through 441 Processing sheet with id= T, first strand: chain 'A' and resid 673 through 678 removed outlier: 6.384A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 693 through 697 removed outlier: 3.919A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 699 through 710 removed outlier: 6.085A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.499A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 1063 through 1065 Processing sheet with id= Y, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.968A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 52 through 59 removed outlier: 4.023A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 67 through 70 removed outlier: 3.609A pdb=" N GLU C 93 " --> pdb=" O HIS C 181 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 230 through 234 removed outlier: 3.767A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 298 through 301 Processing sheet with id= AD, first strand: chain 'C' and resid 312 through 315 removed outlier: 8.527A pdb=" N VAL C 313 " --> pdb=" O CYS C 524 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASN C 526 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ARG C 315 " --> pdb=" O ASN C 526 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN C 528 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 341 through 345 removed outlier: 4.175A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 438 through 441 removed outlier: 4.639A pdb=" N TYR C 438 " --> pdb=" O TYR C 481 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 673 through 678 removed outlier: 6.465A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 693 through 697 removed outlier: 3.975A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 699 through 710 removed outlier: 6.074A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id= AJ, 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= AK, first strand: chain 'C' and resid 1063 through 1065 891 hydrogen bonds defined for protein. 2466 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: 11.27 Time building geometry restraints manager: 9.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.33: 4683 1.33 - 1.48: 10003 1.48 - 1.63: 10687 1.63 - 1.78: 22 1.78 - 1.93: 167 Bond restraints: 25562 Sorted by residual: bond pdb=" ND BLA B1318 " pdb=" C1D BLA B1318 " ideal model delta sigma weight residual 1.319 1.484 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" ND BLA C1317 " pdb=" C1D BLA C1317 " ideal model delta sigma weight residual 1.319 1.481 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" C1C BLA B1318 " pdb=" NC BLA B1318 " ideal model delta sigma weight residual 1.368 1.530 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" ND BLA A1317 " pdb=" C1D BLA A1317 " ideal model delta sigma weight residual 1.319 1.481 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C4C BLA C1317 " pdb=" NC BLA C1317 " ideal model delta sigma weight residual 1.375 1.535 -0.160 2.00e-02 2.50e+03 6.39e+01 ... (remaining 25557 not shown) Histogram of bond angle deviations from ideal: 98.18 - 106.41: 657 106.41 - 114.63: 14970 114.63 - 122.85: 16355 122.85 - 131.07: 2712 131.07 - 139.29: 50 Bond angle restraints: 34744 Sorted by residual: angle pdb=" CA CYS C 366 " pdb=" CB CYS C 366 " pdb=" SG CYS C 366 " ideal model delta sigma weight residual 114.40 139.29 -24.89 2.30e+00 1.89e-01 1.17e+02 angle pdb=" CA CYS B 159 " pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " ideal model delta sigma weight residual 114.40 132.91 -18.51 2.30e+00 1.89e-01 6.48e+01 angle pdb=" C CYS A 467 " pdb=" N THR A 468 " pdb=" CA THR A 468 " ideal model delta sigma weight residual 120.49 128.80 -8.31 1.42e+00 4.96e-01 3.42e+01 angle pdb=" N CYS C 366 " pdb=" CA CYS C 366 " pdb=" C CYS C 366 " ideal model delta sigma weight residual 108.96 116.53 -7.57 1.49e+00 4.50e-01 2.58e+01 angle pdb=" C ASN B 158 " pdb=" N CYS B 159 " pdb=" CA CYS B 159 " ideal model delta sigma weight residual 122.81 114.43 8.38 1.68e+00 3.54e-01 2.49e+01 ... (remaining 34739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13499 17.99 - 35.97: 1076 35.97 - 53.96: 182 53.96 - 71.94: 45 71.94 - 89.93: 16 Dihedral angle restraints: 14818 sinusoidal: 5808 harmonic: 9010 Sorted by residual: dihedral pdb=" CB CYS C1064 " pdb=" SG CYS C1064 " pdb=" SG CYS C1108 " pdb=" CB CYS C1108 " ideal model delta sinusoidal sigma weight residual -86.00 -0.55 -85.45 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" CB CYS A1064 " pdb=" SG CYS A1064 " pdb=" SG CYS A1108 " pdb=" CB CYS A1108 " ideal model delta sinusoidal sigma weight residual -86.00 -3.97 -82.03 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS B 648 " pdb=" SG CYS B 648 " pdb=" SG CYS B 657 " pdb=" CB CYS B 657 " ideal model delta sinusoidal sigma weight residual -86.00 -5.56 -80.44 1 1.00e+01 1.00e-02 8.01e+01 ... (remaining 14815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3551 0.088 - 0.176: 448 0.176 - 0.264: 14 0.264 - 0.352: 6 0.352 - 0.440: 8 Chirality restraints: 4027 Sorted by residual: chirality pdb=" C1 NAG B1315 " pdb=" ND2 ASN B 699 " pdb=" C2 NAG B1315 " pdb=" O5 NAG B1315 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" C1 NAG A1314 " pdb=" ND2 ASN A 699 " pdb=" C2 NAG A1314 " pdb=" O5 NAG A1314 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CB ILE C 152 " pdb=" CA ILE C 152 " pdb=" CG1 ILE C 152 " pdb=" CG2 ILE C 152 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 4024 not shown) Planarity restraints: 4468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA B1318 " -0.223 2.00e-02 2.50e+03 2.75e-01 1.89e+03 pdb=" C1A BLA B1318 " 0.643 2.00e-02 2.50e+03 pdb=" C1D BLA B1318 " -0.037 2.00e-02 2.50e+03 pdb=" C2D BLA B1318 " 0.061 2.00e-02 2.50e+03 pdb=" C3D BLA B1318 " -0.071 2.00e-02 2.50e+03 pdb=" C4D BLA B1318 " -0.252 2.00e-02 2.50e+03 pdb=" CAD BLA B1318 " -0.026 2.00e-02 2.50e+03 pdb=" CHA BLA B1318 " -0.393 2.00e-02 2.50e+03 pdb=" CHD BLA B1318 " 0.046 2.00e-02 2.50e+03 pdb=" CMD BLA B1318 " 0.252 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BLA B1318 " -0.021 2.00e-02 2.50e+03 1.46e-01 5.30e+02 pdb=" C1D BLA B1318 " 0.331 2.00e-02 2.50e+03 pdb=" C2C BLA B1318 " 0.031 2.00e-02 2.50e+03 pdb=" C3C BLA B1318 " -0.030 2.00e-02 2.50e+03 pdb=" C4C BLA B1318 " -0.132 2.00e-02 2.50e+03 pdb=" CAC BLA B1318 " 0.000 2.00e-02 2.50e+03 pdb=" CHD BLA B1318 " -0.212 2.00e-02 2.50e+03 pdb=" CMC BLA B1318 " 0.146 2.00e-02 2.50e+03 pdb=" NC BLA B1318 " -0.127 2.00e-02 2.50e+03 pdb=" OC BLA B1318 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA C1317 " -0.098 2.00e-02 2.50e+03 1.12e-01 3.11e+02 pdb=" C1A BLA C1317 " 0.253 2.00e-02 2.50e+03 pdb=" C1D BLA C1317 " -0.021 2.00e-02 2.50e+03 pdb=" C2D BLA C1317 " 0.028 2.00e-02 2.50e+03 pdb=" C3D BLA C1317 " -0.023 2.00e-02 2.50e+03 pdb=" C4D BLA C1317 " -0.101 2.00e-02 2.50e+03 pdb=" CAD BLA C1317 " 0.008 2.00e-02 2.50e+03 pdb=" CHA BLA C1317 " -0.162 2.00e-02 2.50e+03 pdb=" CHD BLA C1317 " 0.005 2.00e-02 2.50e+03 pdb=" CMD BLA C1317 " 0.111 2.00e-02 2.50e+03 ... (remaining 4465 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6284 2.80 - 3.32: 20049 3.32 - 3.85: 38899 3.85 - 4.37: 46369 4.37 - 4.90: 82316 Nonbonded interactions: 193917 Sorted by model distance: nonbonded pdb=" OH TYR C 436 " pdb=" OH TYR C 484 " model vdw 2.274 2.440 nonbonded pdb=" OG1 THR A 894 " pdb=" OD1 ASN A 896 " model vdw 2.305 2.440 nonbonded pdb=" OH TYR A 436 " pdb=" OH TYR A 484 " model vdw 2.312 2.440 nonbonded pdb=" OG SER C 461 " pdb=" OD1 ASP C 463 " model vdw 2.315 2.440 nonbonded pdb=" O ASN A 960 " pdb=" OG SER A 964 " model vdw 2.323 2.440 ... (remaining 193912 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 93 or resid 96 through 250 or resid 252 through \ 603 or resid 619 through 810 or resid 815 through 823 or resid 829 through 1123 \ or resid 1301 through 1316)) selection = (chain 'B' and (resid 31 through 1123 or resid 1301 through 1316)) selection = (chain 'C' and (resid 31 through 93 or resid 96 through 250 or resid 252 through \ 810 or resid 815 through 823 or resid 829 through 1123 or resid 1301 through 13 \ 16)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.650 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: 8.880 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 66.550 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 0.165 25562 Z= 0.511 Angle : 0.852 24.890 34744 Z= 0.444 Chirality : 0.057 0.440 4027 Planarity : 0.008 0.275 4422 Dihedral : 13.298 89.931 8887 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.19 (0.14), residues: 3046 helix: -0.24 (0.19), residues: 697 sheet: 0.66 (0.19), residues: 695 loop : -1.75 (0.13), residues: 1654 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 203 average time/residue: 1.2781 time to fit residues: 306.0383 Evaluate side-chains 154 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 2.976 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 3.5788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 241 optimal weight: 0.0770 chunk 93 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 279 optimal weight: 0.7980 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 984 GLN A 112 GLN A 122 ASN A 987 GLN C 889 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25562 Z= 0.231 Angle : 0.552 13.426 34744 Z= 0.292 Chirality : 0.047 0.316 4027 Planarity : 0.004 0.057 4422 Dihedral : 5.947 78.938 3397 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.46 % Allowed : 6.39 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.72 (0.14), residues: 3046 helix: 0.55 (0.20), residues: 709 sheet: 0.75 (0.19), residues: 696 loop : -1.57 (0.13), residues: 1641 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 167 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 11 residues processed: 188 average time/residue: 1.2249 time to fit residues: 273.9768 Evaluate side-chains 163 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 2.583 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.3115 time to fit residues: 5.1064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 280 optimal weight: 0.0980 chunk 302 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 277 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 904 GLN B 908 GLN A 987 GLN C 917 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 0.074 25562 Z= 0.198 Angle : 0.513 14.413 34744 Z= 0.272 Chirality : 0.046 0.276 4027 Planarity : 0.004 0.055 4422 Dihedral : 5.684 78.982 3397 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.49 % Allowed : 8.36 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.50 (0.14), residues: 3046 helix: 0.97 (0.20), residues: 703 sheet: 0.78 (0.20), residues: 665 loop : -1.44 (0.13), residues: 1678 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 178 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 14 residues processed: 201 average time/residue: 1.1654 time to fit residues: 280.1442 Evaluate side-chains 174 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 2.852 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 3 average time/residue: 0.3487 time to fit residues: 5.2617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 133 optimal weight: 0.0370 chunk 188 optimal weight: 6.9990 chunk 281 optimal weight: 3.9990 chunk 297 optimal weight: 0.4980 chunk 146 optimal weight: 0.7980 chunk 266 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN A 304 ASN A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 25562 Z= 0.153 Angle : 0.474 10.158 34744 Z= 0.252 Chirality : 0.045 0.253 4027 Planarity : 0.004 0.050 4422 Dihedral : 5.303 74.548 3397 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.64 % Allowed : 10.12 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.28 (0.15), residues: 3046 helix: 1.27 (0.20), residues: 707 sheet: 0.78 (0.19), residues: 679 loop : -1.31 (0.13), residues: 1660 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 20 residues processed: 197 average time/residue: 1.1570 time to fit residues: 274.3245 Evaluate side-chains 177 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 2.880 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 2 average time/residue: 0.3693 time to fit residues: 4.6445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 221 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 254 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 267 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 ASN A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 25562 Z= 0.293 Angle : 0.560 16.430 34744 Z= 0.295 Chirality : 0.048 0.306 4027 Planarity : 0.004 0.044 4422 Dihedral : 5.653 81.461 3397 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.45 % Rotamer: Outliers : 1.72 % Allowed : 11.87 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.33 (0.14), residues: 3046 helix: 1.17 (0.20), residues: 695 sheet: 0.87 (0.19), residues: 692 loop : -1.38 (0.13), residues: 1659 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 161 time to evaluate : 4.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 30 residues processed: 197 average time/residue: 1.1969 time to fit residues: 282.8965 Evaluate side-chains 187 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 2.691 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 25 residues processed: 5 average time/residue: 0.4972 time to fit residues: 7.2564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 174 optimal weight: 0.1980 chunk 73 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 247 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 ASN A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25562 Z= 0.289 Angle : 0.559 15.046 34744 Z= 0.295 Chirality : 0.048 0.300 4027 Planarity : 0.004 0.046 4422 Dihedral : 5.665 84.769 3397 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.90 % Allowed : 12.99 % Favored : 85.10 % 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: -0.37 (0.14), residues: 3046 helix: 1.11 (0.20), residues: 696 sheet: 0.83 (0.19), residues: 679 loop : -1.36 (0.13), residues: 1671 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 158 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 38 residues processed: 197 average time/residue: 1.1343 time to fit residues: 267.8199 Evaluate side-chains 189 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 2.947 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 33 residues processed: 5 average time/residue: 0.5898 time to fit residues: 7.5519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 169 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 250 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 296 optimal weight: 0.9990 chunk 185 optimal weight: 7.9990 chunk 180 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN C 889 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25562 Z= 0.211 Angle : 0.512 13.661 34744 Z= 0.271 Chirality : 0.047 0.309 4027 Planarity : 0.004 0.043 4422 Dihedral : 5.421 79.028 3397 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.09 % Allowed : 13.41 % Favored : 84.50 % 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: -0.26 (0.15), residues: 3046 helix: 1.27 (0.20), residues: 701 sheet: 0.84 (0.19), residues: 693 loop : -1.32 (0.14), residues: 1652 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 155 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 36 residues processed: 202 average time/residue: 1.1732 time to fit residues: 287.7595 Evaluate side-chains 185 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 2.830 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 33 residues processed: 3 average time/residue: 0.3081 time to fit residues: 5.3466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 202 optimal weight: 0.4980 chunk 146 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 233 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN A 301 GLN A 987 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 25562 Z= 0.222 Angle : 0.527 16.073 34744 Z= 0.278 Chirality : 0.046 0.283 4027 Planarity : 0.004 0.041 4422 Dihedral : 5.442 77.385 3397 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.87 % Allowed : 13.63 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.22 (0.15), residues: 3046 helix: 1.27 (0.20), residues: 703 sheet: 0.92 (0.19), residues: 675 loop : -1.29 (0.14), residues: 1668 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 161 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 38 residues processed: 202 average time/residue: 1.1072 time to fit residues: 270.3052 Evaluate side-chains 190 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 2.786 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 38 outliers final: 35 residues processed: 4 average time/residue: 0.7500 time to fit residues: 7.4340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 217 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 249 optimal weight: 7.9990 chunk 261 optimal weight: 0.0030 chunk 275 optimal weight: 0.7980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN A 78 ASN A 304 ASN A 987 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 25562 Z= 0.163 Angle : 0.486 15.303 34744 Z= 0.257 Chirality : 0.045 0.262 4027 Planarity : 0.004 0.041 4422 Dihedral : 5.197 73.229 3397 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.53 % Allowed : 13.89 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.12 (0.15), residues: 3046 helix: 1.49 (0.21), residues: 699 sheet: 0.85 (0.19), residues: 677 loop : -1.21 (0.14), residues: 1670 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 164 time to evaluate : 2.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 35 residues processed: 203 average time/residue: 1.1484 time to fit residues: 282.1043 Evaluate side-chains 185 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 150 time to evaluate : 2.610 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 35 outliers final: 35 residues processed: 1 average time/residue: 0.3879 time to fit residues: 4.3350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 0.7980 chunk 292 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 306 optimal weight: 2.9990 chunk 282 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 960 ASN A 78 ASN A 987 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 25562 Z= 0.255 Angle : 0.538 15.833 34744 Z= 0.284 Chirality : 0.047 0.294 4027 Planarity : 0.004 0.042 4422 Dihedral : 5.443 73.554 3397 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.53 % Allowed : 14.15 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3046 helix: 1.38 (0.20), residues: 692 sheet: 0.95 (0.19), residues: 675 loop : -1.25 (0.14), residues: 1679 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6092 Ramachandran restraints generated. 3046 Oldfield, 0 Emsley, 3046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 153 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 37 residues processed: 190 average time/residue: 1.1494 time to fit residues: 262.9387 Evaluate side-chains 185 residues out of total 2678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 2.546 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 37 outliers final: 36 residues processed: 2 average time/residue: 0.3584 time to fit residues: 4.5474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 0.8980 chunk 260 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 225 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 244 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN A 987 GLN C 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.092768 restraints weight = 34806.537| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.39 r_work: 0.2926 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25562 Z= 0.187 Angle : 0.503 15.337 34744 Z= 0.266 Chirality : 0.045 0.276 4027 Planarity : 0.004 0.043 4422 Dihedral : 5.257 71.057 3397 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.57 % Allowed : 14.23 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.12 (0.15), residues: 3046 helix: 1.43 (0.20), residues: 702 sheet: 0.86 (0.19), residues: 676 loop : -1.20 (0.14), residues: 1668 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6196.75 seconds wall clock time: 112 minutes 48.40 seconds (6768.40 seconds total)