Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 03:48:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh1_14717/04_2023/7zh1_14717_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh1_14717/04_2023/7zh1_14717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh1_14717/04_2023/7zh1_14717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh1_14717/04_2023/7zh1_14717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh1_14717/04_2023/7zh1_14717_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh1_14717/04_2023/7zh1_14717_updated.pdb" } resolution = 2.48 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= 0.001 sd= 0.013 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 132 5.16 5 C 15651 2.51 5 N 3996 2.21 5 O 4722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 972": "OE1" <-> "OE2" Residue "A GLU 999": "OE1" <-> "OE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 972": "OE1" <-> "OE2" Residue "B GLU 999": "OE1" <-> "OE2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 972": "OE1" <-> "OE2" Residue "C GLU 999": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 24501 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7979 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 48, 'TRANS': 971} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7979 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 48, 'TRANS': 971} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7979 Classifications: {'peptide': 1020} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 48, 'TRANS': 971} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 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: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 160 Unusual residues: {'EIC': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 14.21, per 1000 atoms: 0.58 Number of scatterers: 24501 At special positions: 0 Unit cell: (128.1, 137.55, 169.05, 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 132 16.00 O 4722 8.00 N 3996 7.00 C 15651 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.02 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=2.06 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.05 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 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 A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.02 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=2.06 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=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.05 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.04 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.02 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.04 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.06 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.05 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 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=2.03 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 A1302 " - " ASN A 109 " " NAG A1303 " - " ASN A 119 " " NAG A1304 " - " ASN A 158 " " NAG A1305 " - " ASN A 269 " " NAG A1306 " - " ASN A 318 " " NAG A1307 " - " ASN A 357 " " NAG A1308 " - " ASN A 602 " " NAG A1310 " - " ASN A 783 " " NAG B1302 " - " ASN B 109 " " NAG B1303 " - " ASN B 119 " " NAG B1304 " - " ASN B 158 " " NAG B1305 " - " ASN B 269 " " NAG B1306 " - " ASN B 318 " " NAG B1307 " - " ASN B 357 " " NAG B1308 " - " ASN B 602 " " NAG B1310 " - " ASN B 783 " " NAG C1302 " - " ASN C 109 " " NAG C1303 " - " ASN C 119 " " NAG C1304 " - " ASN C 158 " " NAG C1305 " - " ASN C 269 " " NAG C1306 " - " ASN C 318 " " NAG C1307 " - " ASN C 357 " " NAG C1308 " - " ASN C 602 " " NAG C1310 " - " ASN C 783 " " NAG D 1 " - " ASN A 227 " " NAG E 1 " - " ASN B 227 " " NAG F 1 " - " ASN C 227 " Time building additional restraints: 10.99 Conformation dependent library (CDL) restraints added in 3.7 seconds 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5742 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 33 sheets defined 22.5% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.87 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 357 removed outlier: 3.538A pdb=" N ASN A 357 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 354 through 357' Processing helix chain 'A' and resid 371 through 376 removed outlier: 4.248A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 removed outlier: 4.128A 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 720 through 723 No H-bonds generated for 'chain 'A' and resid 720 through 723' Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 742 through 764 Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 819 through 824 Processing helix chain 'A' and resid 831 through 838 Processing helix chain 'A' and resid 849 through 864 Processing helix chain 'A' and resid 880 through 891 Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'A' and resid 902 through 921 Processing helix chain 'A' and resid 929 through 949 removed outlier: 6.168A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER A 949 " --> pdb=" O VAL A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 965 Processing helix chain 'A' and resid 968 through 1014 removed outlier: 3.877A pdb=" N VAL A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (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 357 removed outlier: 3.538A pdb=" N ASN B 357 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 357' Processing helix chain 'B' and resid 371 through 376 removed outlier: 4.248A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 396 removed outlier: 4.128A 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 723 No H-bonds generated for 'chain 'B' and resid 720 through 723' Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 742 through 764 Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 819 through 824 Processing helix chain 'B' and resid 831 through 838 Processing helix chain 'B' and resid 849 through 864 Processing helix chain 'B' and resid 880 through 891 Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 902 through 921 Processing helix chain 'B' and resid 929 through 949 removed outlier: 6.168A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER B 949 " --> pdb=" O VAL B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 965 Processing helix chain 'B' and resid 968 through 1014 removed outlier: 3.878A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (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 357 removed outlier: 3.538A pdb=" N ASN C 357 " --> pdb=" O VAL C 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 354 through 357' Processing helix chain 'C' and resid 371 through 376 removed outlier: 4.248A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 396 removed outlier: 4.128A 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 723 No H-bonds generated for 'chain 'C' and resid 720 through 723' Processing helix chain 'C' and resid 729 through 736 Processing helix chain 'C' and resid 742 through 764 Processing helix chain 'C' and resid 799 through 807 Processing helix chain 'C' and resid 819 through 824 Processing helix chain 'C' and resid 831 through 838 Processing helix chain 'C' and resid 849 through 864 Processing helix chain 'C' and resid 880 through 891 Processing helix chain 'C' and resid 895 through 900 Processing helix chain 'C' and resid 902 through 921 Processing helix chain 'C' and resid 929 through 949 removed outlier: 6.168A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 965 Processing helix chain 'C' and resid 968 through 1014 removed outlier: 3.877A pdb=" N VAL C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.716A pdb=" N THR A 31 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 220 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.084A 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: 4.195A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 161 through 164 removed outlier: 5.946A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 298 through 302 removed outlier: 4.351A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 312 through 315 removed outlier: 8.318A pdb=" N VAL A 313 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN A 526 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ARG A 315 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN A 528 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.626A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (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 673 through 678 removed outlier: 6.386A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 693 through 697 removed outlier: 4.244A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 699 through 710 removed outlier: 3.635A pdb=" N MET A1032 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.468A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.716A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 220 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 51 through 59 removed outlier: 4.195A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 161 through 164 removed outlier: 5.946A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 234 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TRP B 101 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG B 232 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE B 103 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN B 230 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 298 through 302 removed outlier: 4.351A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 312 through 315 removed outlier: 8.317A pdb=" N VAL B 313 " --> pdb=" O CYS B 524 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN B 526 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ARG B 315 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN B 528 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.625A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 439 through 441 Processing sheet with id= S, first strand: chain 'B' and resid 673 through 678 removed outlier: 6.387A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 693 through 697 removed outlier: 4.244A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 699 through 710 removed outlier: 3.635A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.469A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 31 through 35 removed outlier: 3.715A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 220 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 51 through 59 removed outlier: 4.194A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 161 through 164 removed outlier: 5.946A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE C 234 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TRP C 101 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARG C 232 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE C 103 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN C 230 " --> pdb=" O PHE C 103 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 298 through 302 removed outlier: 4.352A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 312 through 315 removed outlier: 8.317A pdb=" N VAL C 313 " --> pdb=" O CYS C 524 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN C 526 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ARG C 315 " --> pdb=" O ASN C 526 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN C 528 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.626A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 439 through 441 Processing sheet with id= AD, first strand: chain 'C' and resid 673 through 678 removed outlier: 6.386A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 693 through 697 removed outlier: 4.244A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 699 through 710 removed outlier: 3.635A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.468A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) 900 hydrogen bonds defined for protein. 2520 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.44 Time building geometry restraints manager: 11.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5714 1.33 - 1.46: 6608 1.46 - 1.58: 12557 1.58 - 1.71: 0 1.71 - 1.84: 180 Bond restraints: 25059 Sorted by residual: bond pdb=" N ILE A 428 " pdb=" CA ILE A 428 " ideal model delta sigma weight residual 1.452 1.498 -0.046 1.18e-02 7.18e+03 1.52e+01 bond pdb=" N ILE C 428 " pdb=" CA ILE C 428 " ideal model delta sigma weight residual 1.452 1.498 -0.046 1.18e-02 7.18e+03 1.51e+01 bond pdb=" N ILE B 428 " pdb=" CA ILE B 428 " ideal model delta sigma weight residual 1.452 1.498 -0.046 1.18e-02 7.18e+03 1.51e+01 bond pdb=" N CYS A 159 " pdb=" CA CYS A 159 " ideal model delta sigma weight residual 1.456 1.500 -0.043 1.22e-02 6.72e+03 1.26e+01 bond pdb=" N CYS C 159 " pdb=" CA CYS C 159 " ideal model delta sigma weight residual 1.456 1.500 -0.043 1.22e-02 6.72e+03 1.25e+01 ... (remaining 25054 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.46: 672 106.46 - 113.38: 13221 113.38 - 120.31: 9468 120.31 - 127.23: 10433 127.23 - 134.16: 253 Bond angle restraints: 34047 Sorted by residual: angle pdb=" O LYS C 929 " pdb=" C LYS C 929 " pdb=" N LEU C 930 " ideal model delta sigma weight residual 122.07 128.54 -6.47 1.03e+00 9.43e-01 3.95e+01 angle pdb=" O LYS A 929 " pdb=" C LYS A 929 " pdb=" N LEU A 930 " ideal model delta sigma weight residual 122.07 128.51 -6.44 1.03e+00 9.43e-01 3.91e+01 angle pdb=" O LYS B 929 " pdb=" C LYS B 929 " pdb=" N LEU B 930 " ideal model delta sigma weight residual 122.07 128.49 -6.42 1.03e+00 9.43e-01 3.89e+01 angle pdb=" CA LYS B 929 " pdb=" C LYS B 929 " pdb=" N LEU B 930 " ideal model delta sigma weight residual 117.07 110.50 6.57 1.14e+00 7.69e-01 3.32e+01 angle pdb=" CA LYS C 929 " pdb=" C LYS C 929 " pdb=" N LEU C 930 " ideal model delta sigma weight residual 117.07 110.50 6.57 1.14e+00 7.69e-01 3.32e+01 ... (remaining 34042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 12852 17.74 - 35.48: 1233 35.48 - 53.22: 392 53.22 - 70.95: 88 70.95 - 88.69: 39 Dihedral angle restraints: 14604 sinusoidal: 5679 harmonic: 8925 Sorted by residual: dihedral pdb=" CB CYS C 725 " pdb=" SG CYS C 725 " pdb=" SG CYS C 731 " pdb=" CB CYS C 731 " ideal model delta sinusoidal sigma weight residual -86.00 -55.84 -30.16 1 1.00e+01 1.00e-02 1.30e+01 dihedral pdb=" CB CYS B 725 " pdb=" SG CYS B 725 " pdb=" SG CYS B 731 " pdb=" CB CYS B 731 " ideal model delta sinusoidal sigma weight residual -86.00 -55.85 -30.15 1 1.00e+01 1.00e-02 1.30e+01 dihedral pdb=" CB CYS A 725 " pdb=" SG CYS A 725 " pdb=" SG CYS A 731 " pdb=" CB CYS A 731 " ideal model delta sinusoidal sigma weight residual -86.00 -55.86 -30.14 1 1.00e+01 1.00e-02 1.30e+01 ... (remaining 14601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 3800 0.172 - 0.344: 105 0.344 - 0.516: 13 0.516 - 0.688: 0 0.688 - 0.860: 3 Chirality restraints: 3921 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 -2.57 0.17 2.00e-02 2.50e+03 7.00e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.97e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.92e+01 ... (remaining 3918 not shown) Planarity restraints: 4386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1310 " -0.350 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG C1310 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C1310 " -0.158 2.00e-02 2.50e+03 pdb=" N2 NAG C1310 " 0.532 2.00e-02 2.50e+03 pdb=" O7 NAG C1310 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1310 " 0.350 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG B1310 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B1310 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG B1310 " -0.532 2.00e-02 2.50e+03 pdb=" O7 NAG B1310 " 0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1310 " -0.350 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG A1310 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG A1310 " -0.158 2.00e-02 2.50e+03 pdb=" N2 NAG A1310 " 0.532 2.00e-02 2.50e+03 pdb=" O7 NAG A1310 " -0.110 2.00e-02 2.50e+03 ... (remaining 4383 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 443 2.68 - 3.23: 21887 3.23 - 3.79: 35121 3.79 - 4.34: 50056 4.34 - 4.90: 82652 Nonbonded interactions: 190159 Sorted by model distance: nonbonded pdb=" ND2 ASN A 699 " pdb=" C1 NAG A1309 " model vdw 2.120 3.550 nonbonded pdb=" ND2 ASN B 699 " pdb=" C1 NAG B1309 " model vdw 2.120 3.550 nonbonded pdb=" ND2 ASN C 699 " pdb=" C1 NAG C1309 " model vdw 2.121 3.550 nonbonded pdb=" O SER C 740 " pdb=" OG SER C 740 " model vdw 2.159 2.440 nonbonded pdb=" O SER A 740 " pdb=" OG SER A 740 " model vdw 2.160 2.440 ... (remaining 190154 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 4.630 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 65.670 Find NCS groups from input model: 1.430 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:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.046 25059 Z= 0.476 Angle : 1.144 12.254 34047 Z= 0.724 Chirality : 0.074 0.860 3921 Planarity : 0.016 0.300 4359 Dihedral : 16.656 88.692 8763 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.31 % Favored : 95.20 % Rotamer Outliers : 2.38 % 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: -0.18 (0.14), residues: 3018 helix: 1.35 (0.18), residues: 732 sheet: 1.31 (0.22), residues: 513 loop : -1.27 (0.12), residues: 1773 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 338 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 18 residues processed: 377 average time/residue: 1.3107 time to fit residues: 571.6364 Evaluate side-chains 287 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 269 time to evaluate : 2.826 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 7 average time/residue: 0.8494 time to fit residues: 11.0470 ------------------------------------------------------------------------------- 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: 3.9990 chunk 231 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 277 optimal weight: 0.0010 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 280 GLN A 473 ASN A 737 GLN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN A 895 GLN A 904 GLN A1056 ASN B 737 GLN B 827 ASN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1056 ASN C 32 GLN C 122 ASN C 280 GLN C 473 ASN C 737 GLN C 744 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1040 HIS C1056 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.102 25059 Z= 0.249 Angle : 0.691 9.371 34047 Z= 0.371 Chirality : 0.050 0.279 3921 Planarity : 0.005 0.041 4359 Dihedral : 5.864 59.344 3333 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.81 % Favored : 95.99 % Rotamer Outliers : 3.33 % 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: 0.02 (0.14), residues: 3018 helix: 1.75 (0.19), residues: 735 sheet: 1.05 (0.19), residues: 663 loop : -1.34 (0.13), residues: 1620 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 292 time to evaluate : 2.995 Fit side-chains revert: symmetry clash outliers start: 88 outliers final: 33 residues processed: 350 average time/residue: 1.3363 time to fit residues: 541.0991 Evaluate side-chains 307 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 274 time to evaluate : 2.810 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 20 residues processed: 13 average time/residue: 0.6234 time to fit residues: 14.3531 ------------------------------------------------------------------------------- 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: 2.9990 chunk 86 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 189 optimal weight: 0.1980 chunk 76 optimal weight: 10.0000 chunk 278 optimal weight: 0.0060 chunk 300 optimal weight: 10.0000 chunk 247 optimal weight: 8.9990 chunk 276 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 overall best weight: 2.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 473 ASN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN A1056 ASN B 122 ASN B 129 ASN B 201 GLN B 280 GLN B 473 ASN B 827 ASN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 GLN B1056 ASN B1065 HIS C 304 ASN C 473 ASN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 915 GLN C 917 GLN C1040 HIS C1053 GLN C1056 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 25059 Z= 0.206 Angle : 0.615 9.627 34047 Z= 0.331 Chirality : 0.046 0.205 3921 Planarity : 0.004 0.037 4359 Dihedral : 5.732 55.769 3333 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.84 % Favored : 95.96 % Rotamer Outliers : 3.48 % 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: -0.12 (0.14), residues: 3018 helix: 1.62 (0.19), residues: 756 sheet: 1.17 (0.20), residues: 597 loop : -1.46 (0.12), residues: 1665 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 275 time to evaluate : 2.796 Fit side-chains revert: symmetry clash outliers start: 92 outliers final: 45 residues processed: 336 average time/residue: 1.3554 time to fit residues: 526.6176 Evaluate side-chains 309 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 264 time to evaluate : 2.963 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 29 residues processed: 16 average time/residue: 0.5883 time to fit residues: 16.6030 ------------------------------------------------------------------------------- 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: 9.9990 chunk 209 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 295 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 201 GLN A 304 ASN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 GLN A 915 GLN A 937 ASN A1056 ASN B 122 ASN B 181 HIS B 473 ASN B 827 ASN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 ASN B 915 GLN B1056 ASN C 129 ASN C 304 ASN C 473 ASN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1040 HIS C1056 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 25059 Z= 0.226 Angle : 0.634 8.245 34047 Z= 0.342 Chirality : 0.047 0.241 3921 Planarity : 0.005 0.040 4359 Dihedral : 5.874 59.640 3333 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.84 % Favored : 95.96 % Rotamer Outliers : 3.59 % 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 (0.14), residues: 3018 helix: 1.42 (0.19), residues: 753 sheet: 0.97 (0.20), residues: 615 loop : -1.53 (0.13), residues: 1650 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 272 time to evaluate : 2.988 Fit side-chains outliers start: 95 outliers final: 46 residues processed: 337 average time/residue: 1.3661 time to fit residues: 532.6324 Evaluate side-chains 310 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 264 time to evaluate : 2.726 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 33 residues processed: 13 average time/residue: 0.5357 time to fit residues: 13.1627 ------------------------------------------------------------------------------- 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: 9.9990 chunk 167 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 GLN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 ASN A1040 HIS A1056 ASN B 181 HIS B 473 ASN B 827 ASN B 901 ASN B1056 ASN C 129 ASN C 473 ASN C 895 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C1040 HIS C1056 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.094 25059 Z= 0.432 Angle : 0.855 11.705 34047 Z= 0.464 Chirality : 0.056 0.194 3921 Planarity : 0.006 0.053 4359 Dihedral : 6.720 59.863 3333 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.47 % Favored : 95.39 % Rotamer Outliers : 3.70 % 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: -0.71 (0.14), residues: 3018 helix: 0.86 (0.18), residues: 732 sheet: 1.05 (0.20), residues: 636 loop : -1.83 (0.12), residues: 1650 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 261 time to evaluate : 3.181 Fit side-chains outliers start: 98 outliers final: 56 residues processed: 333 average time/residue: 1.3486 time to fit residues: 519.5989 Evaluate side-chains 310 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 254 time to evaluate : 2.848 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 44 residues processed: 12 average time/residue: 0.8122 time to fit residues: 16.0127 ------------------------------------------------------------------------------- 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: 0.3980 chunk 266 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 173 optimal weight: 0.0060 chunk 73 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 245 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 GLN A 937 ASN A1053 GLN B 181 HIS B 473 ASN B 827 ASN B 901 ASN B1056 ASN C 473 ASN C 769 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 889 ASN C 895 GLN C1040 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 25059 Z= 0.162 Angle : 0.555 8.011 34047 Z= 0.300 Chirality : 0.044 0.194 3921 Planarity : 0.004 0.040 4359 Dihedral : 6.095 59.367 3333 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.45 % Rotamer Outliers : 2.72 % 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: 3018 helix: 1.53 (0.19), residues: 732 sheet: 1.04 (0.20), residues: 603 loop : -1.65 (0.13), residues: 1683 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 270 time to evaluate : 3.016 Fit side-chains outliers start: 72 outliers final: 44 residues processed: 326 average time/residue: 1.3944 time to fit residues: 527.8219 Evaluate side-chains 299 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 255 time to evaluate : 3.073 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 40 residues processed: 5 average time/residue: 1.0872 time to fit residues: 10.8889 ------------------------------------------------------------------------------- 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: 9.9990 chunk 33 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 249 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN A 937 ASN B 181 HIS B 473 ASN B 505 ASN B 827 ASN B 901 ASN B1056 ASN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 473 ASN C 769 GLN C 904 GLN C 917 GLN C1040 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 25059 Z= 0.269 Angle : 0.676 10.716 34047 Z= 0.366 Chirality : 0.048 0.180 3921 Planarity : 0.005 0.042 4359 Dihedral : 6.292 58.144 3333 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.27 % Favored : 95.59 % Rotamer Outliers : 2.91 % 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: -0.55 (0.14), residues: 3018 helix: 1.29 (0.19), residues: 729 sheet: 0.88 (0.20), residues: 612 loop : -1.70 (0.12), residues: 1677 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 254 time to evaluate : 2.936 Fit side-chains outliers start: 77 outliers final: 53 residues processed: 311 average time/residue: 1.3540 time to fit residues: 487.6134 Evaluate side-chains 307 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 254 time to evaluate : 2.951 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 45 residues processed: 9 average time/residue: 0.7996 time to fit residues: 13.1285 ------------------------------------------------------------------------------- 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: 9.9990 chunk 117 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 ASN B 181 HIS B 473 ASN B 827 ASN B 901 ASN B1056 ASN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 201 GLN C 473 ASN C 769 GLN C 895 GLN C 908 GLN C 917 GLN C1040 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.093 25059 Z= 0.420 Angle : 0.843 14.126 34047 Z= 0.459 Chirality : 0.055 0.212 3921 Planarity : 0.006 0.053 4359 Dihedral : 6.678 57.581 3333 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.10 % Favored : 94.80 % Rotamer Outliers : 2.95 % 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: -0.84 (0.14), residues: 3018 helix: 0.77 (0.18), residues: 732 sheet: 0.74 (0.19), residues: 675 loop : -1.87 (0.12), residues: 1611 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 252 time to evaluate : 3.182 Fit side-chains outliers start: 78 outliers final: 56 residues processed: 313 average time/residue: 1.4021 time to fit residues: 509.5538 Evaluate side-chains 308 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 252 time to evaluate : 2.976 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 48 residues processed: 9 average time/residue: 0.4184 time to fit residues: 9.7422 ------------------------------------------------------------------------------- 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: 4.9990 chunk 257 optimal weight: 10.0000 chunk 274 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 119 optimal weight: 0.3980 chunk 215 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 259 optimal weight: 0.0770 chunk 273 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN A 917 GLN A 937 ASN B 181 HIS B 473 ASN B 827 ASN B 915 GLN C 32 GLN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN C 769 GLN C 889 ASN C 895 GLN C1040 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 25059 Z= 0.146 Angle : 0.533 9.339 34047 Z= 0.287 Chirality : 0.043 0.181 3921 Planarity : 0.004 0.044 4359 Dihedral : 5.753 58.807 3333 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % Rotamer Outliers : 2.19 % 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 (0.14), residues: 3018 helix: 1.73 (0.19), residues: 708 sheet: 0.91 (0.19), residues: 663 loop : -1.60 (0.13), residues: 1647 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 273 time to evaluate : 2.923 Fit side-chains outliers start: 58 outliers final: 41 residues processed: 327 average time/residue: 1.4152 time to fit residues: 535.9496 Evaluate side-chains 304 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 263 time to evaluate : 3.054 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 40 residues processed: 2 average time/residue: 1.4722 time to fit residues: 7.2440 ------------------------------------------------------------------------------- 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: 10.0000 chunk 177 optimal weight: 0.6980 chunk 137 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 304 optimal weight: 0.0670 chunk 280 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 192 optimal weight: 7.9990 overall best weight: 2.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN A 937 ASN B 181 HIS B 473 ASN B 827 ASN B 915 GLN B1056 ASN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 473 ASN C 769 GLN C 895 GLN C1040 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 25059 Z= 0.206 Angle : 0.603 11.503 34047 Z= 0.327 Chirality : 0.046 0.184 3921 Planarity : 0.004 0.040 4359 Dihedral : 5.909 58.410 3333 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Rotamer Outliers : 2.04 % 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: 3018 helix: 1.57 (0.19), residues: 726 sheet: 0.95 (0.19), residues: 654 loop : -1.70 (0.13), residues: 1638 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 264 time to evaluate : 3.100 Fit side-chains outliers start: 54 outliers final: 44 residues processed: 312 average time/residue: 1.4271 time to fit residues: 515.1133 Evaluate side-chains 301 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 257 time to evaluate : 2.917 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 43 residues processed: 2 average time/residue: 1.0185 time to fit residues: 6.3588 ------------------------------------------------------------------------------- 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: 10.0000 chunk 74 optimal weight: 6.9990 chunk 223 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 249 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 213 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN A 937 ASN B 181 HIS B 473 ASN B 827 ASN B 901 ASN B1056 ASN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 473 ASN C 769 GLN C1040 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115663 restraints weight = 25782.583| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.67 r_work: 0.3035 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 25059 Z= 0.316 Angle : 0.724 13.306 34047 Z= 0.396 Chirality : 0.050 0.200 3921 Planarity : 0.005 0.043 4359 Dihedral : 6.316 59.986 3333 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.06 % Rotamer Outliers : 2.04 % 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: -0.60 (0.14), residues: 3018 helix: 1.11 (0.19), residues: 732 sheet: 0.89 (0.20), residues: 642 loop : -1.74 (0.13), residues: 1644 =============================================================================== Job complete usr+sys time: 8457.59 seconds wall clock time: 151 minutes 35.96 seconds (9095.96 seconds total)