Starting phenix.real_space_refine on Mon Feb 19 11:03:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh1_14717/02_2024/7zh1_14717_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh1_14717/02_2024/7zh1_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_14717/02_2024/7zh1_14717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh1_14717/02_2024/7zh1_14717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh1_14717/02_2024/7zh1_14717_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh1_14717/02_2024/7zh1_14717_updated.pdb" } resolution = 2.48 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= 0.001 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-dev-5238/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 30 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 dihedrals: 30 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 12.76, per 1000 atoms: 0.52 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: 9.73 Conformation dependent library (CDL) restraints added in 4.3 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: 6.15 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: 9.66 Time building geometry restraints manager: 10.53 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: 13539 17.74 - 35.48: 1260 35.48 - 53.22: 422 53.22 - 70.95: 100 70.95 - 88.69: 39 Dihedral angle restraints: 15360 sinusoidal: 6435 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 15357 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: 0.500 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: 3.610 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 65.240 Find NCS groups from input model: 1.410 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: 0.000 Load rotamer database and sin/cos tables:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.500 ------------------------------------------------------------------------------- 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 : 16.416 88.692 9519 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 % Allowed : 18.33 % Favored : 79.29 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 868 HIS 0.006 0.002 HIS C1046 PHE 0.086 0.002 PHE B 784 TYR 0.047 0.003 TYR A1070 ARG 0.010 0.001 ARG A 758 *********************** 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 : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ILE cc_start: 0.8392 (mm) cc_final: 0.7984 (mm) REVERT: A 504 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8101 (mt) REVERT: A 816 MET cc_start: 0.8335 (ttp) cc_final: 0.8057 (ttp) REVERT: B 96 ASN cc_start: 0.6405 (OUTLIER) cc_final: 0.5799 (p0) REVERT: B 164 ILE cc_start: 0.8557 (mm) cc_final: 0.8188 (mm) REVERT: B 449 ARG cc_start: 0.7807 (mtp180) cc_final: 0.7427 (mtm180) REVERT: B 741 PHE cc_start: 0.6173 (m-80) cc_final: 0.5724 (m-80) REVERT: B 917 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.6578 (tm-30) REVERT: B 1098 THR cc_start: 0.5697 (m) cc_final: 0.5304 (p) REVERT: C 96 ASN cc_start: 0.6527 (OUTLIER) cc_final: 0.5631 (p0) REVERT: C 99 ARG cc_start: 0.8242 (mmt90) cc_final: 0.8004 (mmt180) REVERT: C 201 GLN cc_start: 0.7023 (tt0) cc_final: 0.6793 (tt0) REVERT: C 741 PHE cc_start: 0.6157 (m-80) cc_final: 0.5577 (m-80) REVERT: C 889 ASN cc_start: 0.7919 (m110) cc_final: 0.7637 (m110) REVERT: C 1085 PHE cc_start: 0.6801 (m-80) cc_final: 0.6415 (m-80) outliers start: 63 outliers final: 18 residues processed: 377 average time/residue: 1.2774 time to fit residues: 557.7684 Evaluate side-chains 292 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 270 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 883 GLN Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1064 CYS Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 1064 CYS Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 1064 CYS 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: 0.9980 chunk 128 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 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: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 473 ASN A 737 GLN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A 904 GLN A1056 ASN B 122 ASN B 737 GLN B 827 ASN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25059 Z= 0.217 Angle : 0.649 9.015 34047 Z= 0.349 Chirality : 0.048 0.271 3921 Planarity : 0.004 0.042 4359 Dihedral : 8.230 78.984 4134 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.55 % Favored : 96.26 % Rotamer: Outliers : 2.76 % Allowed : 18.63 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3018 helix: 1.97 (0.19), residues: 729 sheet: 1.30 (0.19), residues: 636 loop : -1.32 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 423 HIS 0.008 0.001 HIS B1046 PHE 0.021 0.002 PHE C 805 TYR 0.023 0.002 TYR A 367 ARG 0.007 0.001 ARG B 426 *********************** 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 364 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 291 time to evaluate : 3.131 Fit side-chains REVERT: A 258 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7595 (mttp) REVERT: A 449 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7735 (mtp180) REVERT: A 959 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8143 (tt) REVERT: A 1088 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6946 (mt0) REVERT: B 258 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7486 (mmtp) REVERT: B 268 GLU cc_start: 0.7268 (pp20) cc_final: 0.6967 (pp20) REVERT: B 449 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7700 (mtp180) REVERT: B 546 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7665 (mm110) REVERT: B 911 LYS cc_start: 0.7481 (ttmp) cc_final: 0.7119 (tttt) REVERT: B 959 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8229 (tt) REVERT: B 1032 MET cc_start: 0.8197 (ptm) cc_final: 0.7982 (ptp) REVERT: B 1098 THR cc_start: 0.5826 (m) cc_final: 0.5243 (p) REVERT: C 201 GLN cc_start: 0.7013 (tt0) cc_final: 0.6773 (tt0) REVERT: C 417 MET cc_start: 0.8751 (ttm) cc_final: 0.8405 (ttp) REVERT: C 449 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7681 (mtp180) REVERT: C 491 TYR cc_start: 0.7319 (m-80) cc_final: 0.6234 (t80) REVERT: C 546 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7724 (mm110) REVERT: C 877 GLN cc_start: 0.5290 (OUTLIER) cc_final: 0.4938 (tp-100) REVERT: C 911 LYS cc_start: 0.7459 (ttmm) cc_final: 0.7166 (tttt) REVERT: C 917 GLN cc_start: 0.7365 (tt0) cc_final: 0.7095 (mt0) REVERT: C 996 ARG cc_start: 0.8302 (mtt-85) cc_final: 0.8014 (mtt180) REVERT: C 1085 PHE cc_start: 0.7030 (m-80) cc_final: 0.6680 (m-80) REVERT: C 1088 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6826 (pt0) REVERT: C 1098 THR cc_start: 0.6143 (m) cc_final: 0.5590 (p) outliers start: 73 outliers final: 22 residues processed: 337 average time/residue: 1.3405 time to fit residues: 521.2467 Evaluate side-chains 307 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 273 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 449 ARG Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 1088 GLN 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: 9.9990 chunk 231 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 278 optimal weight: 0.0270 chunk 300 optimal weight: 10.0000 chunk 247 optimal weight: 8.9990 chunk 276 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 223 optimal weight: 10.0000 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 280 GLN A 304 ASN A 473 ASN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 473 ASN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1040 HIS C1053 GLN C1056 ASN C1065 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 25059 Z= 0.234 Angle : 0.653 10.866 34047 Z= 0.354 Chirality : 0.048 0.196 3921 Planarity : 0.005 0.037 4359 Dihedral : 7.735 70.537 4098 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.91 % Favored : 95.89 % Rotamer: Outliers : 3.21 % Allowed : 16.89 % Favored : 79.89 % 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: -0.21 (0.14), residues: 3018 helix: 1.52 (0.19), residues: 756 sheet: 0.98 (0.20), residues: 612 loop : -1.46 (0.12), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 423 HIS 0.008 0.002 HIS B1046 PHE 0.022 0.002 PHE B 805 TYR 0.027 0.002 TYR A 367 ARG 0.006 0.001 ARG A1055 *********************** 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: 85 poor density : 282 time to evaluate : 2.702 Fit side-chains REVERT: A 258 LYS cc_start: 0.7940 (mtpp) cc_final: 0.7641 (mttp) REVERT: A 449 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7767 (mtp180) REVERT: A 546 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: A 679 MET cc_start: 0.7598 (mtp) cc_final: 0.7293 (mtp) REVERT: A 959 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8225 (tt) REVERT: A 1088 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6865 (mt0) REVERT: B 258 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7465 (mmtp) REVERT: B 268 GLU cc_start: 0.7368 (pp20) cc_final: 0.7050 (pp20) REVERT: B 449 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7705 (mtp180) REVERT: B 546 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7482 (mt0) REVERT: B 741 PHE cc_start: 0.6202 (m-80) cc_final: 0.5973 (m-80) REVERT: B 784 PHE cc_start: 0.8516 (m-80) cc_final: 0.8311 (m-80) REVERT: B 911 LYS cc_start: 0.7566 (ttmp) cc_final: 0.7242 (tttt) REVERT: B 959 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8388 (tt) REVERT: C 417 MET cc_start: 0.8767 (ttm) cc_final: 0.8406 (ttp) REVERT: C 449 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7730 (mtp180) REVERT: C 514 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8137 (tttm) REVERT: C 877 GLN cc_start: 0.5592 (OUTLIER) cc_final: 0.5099 (tp-100) REVERT: C 996 ARG cc_start: 0.8305 (mtt-85) cc_final: 0.8020 (mtt180) REVERT: C 1085 PHE cc_start: 0.7057 (m-80) cc_final: 0.6723 (m-80) REVERT: C 1088 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6855 (pt0) outliers start: 85 outliers final: 34 residues processed: 336 average time/residue: 1.3544 time to fit residues: 523.5508 Evaluate side-chains 312 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 266 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 449 ARG Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 1088 GLN Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 264 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 937 ASN A1040 HIS A1056 ASN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS B 473 ASN B 827 ASN ** B 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 ASN B1056 ASN C 129 ASN C 201 GLN C 473 ASN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 25059 Z= 0.248 Angle : 0.659 8.797 34047 Z= 0.358 Chirality : 0.048 0.198 3921 Planarity : 0.005 0.041 4359 Dihedral : 7.710 65.154 4098 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.71 % Favored : 96.09 % Rotamer: Outliers : 3.97 % Allowed : 16.48 % Favored : 79.55 % 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: -0.40 (0.14), residues: 3018 helix: 1.30 (0.19), residues: 753 sheet: 0.92 (0.20), residues: 606 loop : -1.56 (0.12), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 423 HIS 0.008 0.001 HIS B1046 PHE 0.018 0.002 PHE B 805 TYR 0.029 0.002 TYR A 367 ARG 0.007 0.001 ARG C1055 *********************** 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 378 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 273 time to evaluate : 2.935 Fit side-chains REVERT: A 56 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: A 258 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7602 (mptt) REVERT: A 449 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7717 (mtp180) REVERT: A 546 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7594 (mt0) REVERT: A 554 ASP cc_start: 0.8111 (p0) cc_final: 0.7911 (p0) REVERT: A 959 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8282 (tt) REVERT: A 1088 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6094 (mm-40) REVERT: B 258 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7484 (mmtp) REVERT: B 268 GLU cc_start: 0.7453 (pp20) cc_final: 0.7186 (pp20) REVERT: B 449 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7729 (mtp180) REVERT: B 514 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8337 (tttp) REVERT: B 741 PHE cc_start: 0.6290 (m-80) cc_final: 0.5926 (m-80) REVERT: B 911 LYS cc_start: 0.7623 (ttmp) cc_final: 0.7414 (ttmm) REVERT: B 959 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8413 (tt) REVERT: B 1020 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7925 (mmtp) REVERT: C 56 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: C 417 MET cc_start: 0.8777 (ttm) cc_final: 0.8375 (ttp) REVERT: C 449 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7750 (mtp180) REVERT: C 514 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8178 (tttm) REVERT: C 546 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7581 (mt0) REVERT: C 877 GLN cc_start: 0.5605 (OUTLIER) cc_final: 0.5157 (tp-100) REVERT: C 996 ARG cc_start: 0.8314 (mtt-85) cc_final: 0.8031 (mtt180) REVERT: C 1020 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7900 (mmtp) REVERT: C 1085 PHE cc_start: 0.7123 (m-80) cc_final: 0.6806 (m-80) REVERT: C 1088 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6777 (pt0) outliers start: 105 outliers final: 42 residues processed: 342 average time/residue: 1.3824 time to fit residues: 544.7006 Evaluate side-chains 324 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 264 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 449 ARG Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 514 LYS Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1088 GLN Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 220 optimal weight: 0.0570 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: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 2.5904 ------------------------------------------------------------------------------- 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 937 ASN A1053 GLN A1056 ASN B 129 ASN B 181 HIS B 473 ASN B 827 ASN B 895 GLN B 901 ASN B1053 GLN B1056 ASN ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C1040 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25059 Z= 0.214 Angle : 0.613 8.638 34047 Z= 0.333 Chirality : 0.046 0.174 3921 Planarity : 0.005 0.042 4359 Dihedral : 7.544 66.707 4098 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 3.36 % Allowed : 16.89 % Favored : 79.74 % 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: -0.38 (0.14), residues: 3018 helix: 1.38 (0.19), residues: 753 sheet: 0.89 (0.20), residues: 612 loop : -1.57 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 423 HIS 0.007 0.001 HIS B1046 PHE 0.015 0.002 PHE C 578 TYR 0.025 0.002 TYR A 367 ARG 0.004 0.001 ARG A 426 *********************** 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 356 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 267 time to evaluate : 2.878 Fit side-chains REVERT: A 56 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: A 258 LYS cc_start: 0.7937 (mtpp) cc_final: 0.7613 (mptt) REVERT: A 449 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7734 (mtp180) REVERT: A 546 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7618 (mt0) REVERT: A 959 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8256 (tt) REVERT: A 1088 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.5941 (mm-40) REVERT: B 258 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7388 (mmtp) REVERT: B 268 GLU cc_start: 0.7453 (pp20) cc_final: 0.7170 (pp20) REVERT: B 449 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7677 (mtp180) REVERT: B 624 THR cc_start: 0.6240 (OUTLIER) cc_final: 0.6002 (t) REVERT: B 741 PHE cc_start: 0.6304 (m-80) cc_final: 0.5929 (m-80) REVERT: B 911 LYS cc_start: 0.7637 (ttmp) cc_final: 0.7106 (mtpp) REVERT: B 959 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8417 (tt) REVERT: B 1020 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7911 (mmtp) REVERT: C 101 TRP cc_start: 0.8837 (OUTLIER) cc_final: 0.7895 (m-90) REVERT: C 417 MET cc_start: 0.8761 (ttm) cc_final: 0.8387 (ttp) REVERT: C 433 THR cc_start: 0.7363 (p) cc_final: 0.7034 (t) REVERT: C 449 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7772 (mtp180) REVERT: C 514 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8184 (tttm) REVERT: C 546 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: C 643 ASP cc_start: 0.6718 (OUTLIER) cc_final: 0.6366 (t0) REVERT: C 877 GLN cc_start: 0.5529 (OUTLIER) cc_final: 0.5082 (tp-100) REVERT: C 996 ARG cc_start: 0.8296 (mtt-85) cc_final: 0.8004 (mtt180) REVERT: C 1020 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7885 (mmtp) REVERT: C 1085 PHE cc_start: 0.7180 (m-80) cc_final: 0.6855 (m-80) REVERT: C 1088 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6746 (pt0) outliers start: 89 outliers final: 46 residues processed: 327 average time/residue: 1.4002 time to fit residues: 524.7109 Evaluate side-chains 325 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 261 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 449 ARG Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 769 GLN Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 951 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1032 MET Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 972 GLU Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1088 GLN Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 8.9990 chunk 266 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 173 optimal weight: 0.7980 chunk 73 optimal weight: 0.0980 chunk 296 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 24 optimal weight: 0.0170 chunk 97 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 overall best weight: 1.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 ASN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS B 473 ASN B 827 ASN B 901 ASN B1056 ASN C 129 ASN C 473 ASN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C1040 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2411 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= 0.167 Angle : 0.548 8.154 34047 Z= 0.297 Chirality : 0.044 0.178 3921 Planarity : 0.004 0.041 4359 Dihedral : 6.997 67.561 4098 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.22 % Rotamer: Outliers : 2.76 % Allowed : 17.72 % Favored : 79.52 % 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: -0.24 (0.14), residues: 3018 helix: 1.57 (0.19), residues: 753 sheet: 0.97 (0.19), residues: 663 loop : -1.60 (0.13), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 423 HIS 0.004 0.001 HIS B1046 PHE 0.013 0.001 PHE A1092 TYR 0.019 0.001 TYR C 352 ARG 0.004 0.000 ARG C1089 *********************** 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 341 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 268 time to evaluate : 3.160 Fit side-chains REVERT: A 258 LYS cc_start: 0.7948 (mtpp) cc_final: 0.7571 (mptt) REVERT: A 546 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7598 (mt0) REVERT: A 572 ASP cc_start: 0.8070 (m-30) cc_final: 0.7802 (m-30) REVERT: A 959 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8238 (tt) REVERT: A 1088 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.5868 (mm-40) REVERT: B 226 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8138 (pt) REVERT: B 258 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7378 (mmtp) REVERT: B 268 GLU cc_start: 0.7432 (pp20) cc_final: 0.7199 (pp20) REVERT: B 449 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7696 (mtp180) REVERT: B 624 THR cc_start: 0.6200 (OUTLIER) cc_final: 0.5969 (t) REVERT: B 741 PHE cc_start: 0.6298 (m-80) cc_final: 0.5910 (m-80) REVERT: B 911 LYS cc_start: 0.7578 (ttmp) cc_final: 0.6987 (mtpp) REVERT: B 959 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8408 (tt) REVERT: B 1020 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7885 (mmtp) REVERT: C 417 MET cc_start: 0.8771 (ttm) cc_final: 0.8431 (ttp) REVERT: C 433 THR cc_start: 0.7303 (p) cc_final: 0.6989 (t) REVERT: C 449 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7816 (mtp180) REVERT: C 514 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8181 (tttm) REVERT: C 546 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7482 (mt0) REVERT: C 643 ASP cc_start: 0.6641 (OUTLIER) cc_final: 0.6323 (t0) REVERT: C 797 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6545 (mtp-110) REVERT: C 877 GLN cc_start: 0.5413 (OUTLIER) cc_final: 0.4954 (tp-100) REVERT: C 996 ARG cc_start: 0.8233 (mtt-85) cc_final: 0.7956 (mtt180) REVERT: C 1020 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7871 (mmtp) REVERT: C 1085 PHE cc_start: 0.7227 (m-80) cc_final: 0.6898 (m-80) REVERT: C 1088 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.5902 (mm-40) outliers start: 73 outliers final: 30 residues processed: 319 average time/residue: 1.3969 time to fit residues: 512.5591 Evaluate side-chains 306 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 259 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 951 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1088 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 249 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 294 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN ** 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 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN C 827 ASN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1040 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25059 Z= 0.196 Angle : 0.583 9.425 34047 Z= 0.316 Chirality : 0.045 0.174 3921 Planarity : 0.004 0.041 4359 Dihedral : 6.868 65.503 4092 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.91 % Favored : 95.99 % Rotamer: Outliers : 3.06 % Allowed : 17.31 % Favored : 79.63 % 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: -0.35 (0.14), residues: 3018 helix: 1.48 (0.19), residues: 750 sheet: 1.04 (0.20), residues: 597 loop : -1.62 (0.13), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 423 HIS 0.006 0.001 HIS B1046 PHE 0.014 0.002 PHE C 578 TYR 0.023 0.002 TYR A 367 ARG 0.003 0.000 ARG C 449 *********************** 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 345 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 264 time to evaluate : 2.893 Fit side-chains REVERT: A 122 ASN cc_start: 0.7611 (m110) cc_final: 0.7351 (m-40) REVERT: A 258 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7615 (mttp) REVERT: A 546 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7599 (mt0) REVERT: A 959 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8233 (tt) REVERT: A 1088 GLN cc_start: 0.6799 (OUTLIER) cc_final: 0.5908 (mm-40) REVERT: B 226 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8152 (pt) REVERT: B 258 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7405 (mmtp) REVERT: B 268 GLU cc_start: 0.7468 (pp20) cc_final: 0.7199 (pp20) REVERT: B 449 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7677 (mtp180) REVERT: B 741 PHE cc_start: 0.6303 (m-80) cc_final: 0.5927 (m-80) REVERT: B 911 LYS cc_start: 0.7636 (ttmp) cc_final: 0.7117 (mtpp) REVERT: B 959 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8422 (tt) REVERT: B 1020 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7887 (mmtp) REVERT: C 56 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: C 417 MET cc_start: 0.8763 (ttm) cc_final: 0.8334 (ttp) REVERT: C 433 THR cc_start: 0.7408 (p) cc_final: 0.6987 (t) REVERT: C 449 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7811 (mtp180) REVERT: C 514 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8187 (tttm) REVERT: C 546 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7485 (mt0) REVERT: C 643 ASP cc_start: 0.6704 (OUTLIER) cc_final: 0.6346 (t0) REVERT: C 797 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6586 (mtp-110) REVERT: C 877 GLN cc_start: 0.5415 (OUTLIER) cc_final: 0.4990 (tp40) REVERT: C 996 ARG cc_start: 0.8272 (mtt-85) cc_final: 0.7984 (mtt180) REVERT: C 1020 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7894 (mmtp) REVERT: C 1085 PHE cc_start: 0.7246 (m-80) cc_final: 0.6923 (m-80) REVERT: C 1088 GLN cc_start: 0.6973 (OUTLIER) cc_final: 0.5877 (mm-40) outliers start: 81 outliers final: 44 residues processed: 326 average time/residue: 1.4152 time to fit residues: 528.5983 Evaluate side-chains 322 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 260 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 951 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1032 MET Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1088 GLN Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 57 optimal weight: 0.0670 chunk 187 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 268 optimal weight: 0.7980 overall best weight: 3.9724 ------------------------------------------------------------------------------- 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 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 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN C 908 GLN C 917 GLN C1040 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 25059 Z= 0.286 Angle : 0.689 11.513 34047 Z= 0.376 Chirality : 0.049 0.236 3921 Planarity : 0.005 0.044 4359 Dihedral : 7.292 64.727 4092 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.63 % Rotamer: Outliers : 3.02 % Allowed : 17.35 % Favored : 79.63 % 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: -0.52 (0.14), residues: 3018 helix: 1.17 (0.19), residues: 747 sheet: 1.03 (0.20), residues: 627 loop : -1.73 (0.13), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 423 HIS 0.009 0.001 HIS B1046 PHE 0.017 0.002 PHE A1092 TYR 0.030 0.002 TYR B 367 ARG 0.005 0.001 ARG A 829 *********************** 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 343 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 263 time to evaluate : 2.652 Fit side-chains REVERT: A 56 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: A 122 ASN cc_start: 0.7659 (m110) cc_final: 0.7413 (m-40) REVERT: A 258 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7530 (mptt) REVERT: A 546 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7744 (mt0) REVERT: A 959 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8289 (tt) REVERT: A 1088 GLN cc_start: 0.6897 (OUTLIER) cc_final: 0.5951 (mm-40) REVERT: B 226 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8182 (pt) REVERT: B 258 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7434 (mmtp) REVERT: B 449 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7668 (mtp180) REVERT: B 727 ASP cc_start: 0.7404 (m-30) cc_final: 0.7079 (m-30) REVERT: B 741 PHE cc_start: 0.6384 (m-80) cc_final: 0.6096 (m-80) REVERT: B 911 LYS cc_start: 0.7703 (ttmp) cc_final: 0.7164 (mtpp) REVERT: B 959 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8449 (tt) REVERT: C 56 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: C 190 LYS cc_start: 0.7954 (tmtt) cc_final: 0.7685 (ttmt) REVERT: C 433 THR cc_start: 0.7477 (p) cc_final: 0.7023 (t) REVERT: C 449 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7772 (mtp180) REVERT: C 514 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8189 (tttm) REVERT: C 546 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7645 (mt0) REVERT: C 643 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6461 (t0) REVERT: C 877 GLN cc_start: 0.5529 (OUTLIER) cc_final: 0.5140 (tp40) REVERT: C 904 GLN cc_start: 0.7808 (tt0) cc_final: 0.7545 (tt0) REVERT: C 1020 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7879 (mmtp) REVERT: C 1085 PHE cc_start: 0.7190 (m-80) cc_final: 0.6924 (m-80) REVERT: C 1088 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6738 (pt0) outliers start: 80 outliers final: 47 residues processed: 325 average time/residue: 1.3616 time to fit residues: 510.4780 Evaluate side-chains 322 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 258 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 951 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 740 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 951 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 1032 MET Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1088 GLN Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 20.0000 chunk 257 optimal weight: 5.9990 chunk 274 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 119 optimal weight: 0.2980 chunk 215 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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 937 ASN B 181 HIS B 473 ASN B 827 ASN B1056 ASN C 32 GLN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN C 769 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C1040 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 25059 Z= 0.239 Angle : 0.634 11.282 34047 Z= 0.347 Chirality : 0.047 0.208 3921 Planarity : 0.005 0.044 4359 Dihedral : 7.038 66.951 4092 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.11 % Favored : 95.79 % Rotamer: Outliers : 2.87 % Allowed : 17.61 % Favored : 79.52 % 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: -0.50 (0.14), residues: 3018 helix: 1.35 (0.19), residues: 729 sheet: 0.86 (0.20), residues: 612 loop : -1.66 (0.13), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 423 HIS 0.008 0.001 HIS B1046 PHE 0.016 0.002 PHE C 578 TYR 0.027 0.002 TYR A 367 ARG 0.004 0.001 ARG A 395 *********************** 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 337 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 261 time to evaluate : 2.775 Fit side-chains REVERT: A 56 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: A 122 ASN cc_start: 0.7592 (m110) cc_final: 0.7329 (m-40) REVERT: A 258 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7596 (mttp) REVERT: A 546 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7718 (mt0) REVERT: A 959 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8271 (tt) REVERT: A 1088 GLN cc_start: 0.6860 (OUTLIER) cc_final: 0.5941 (mm-40) REVERT: B 226 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8166 (pt) REVERT: B 258 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7394 (mmtp) REVERT: B 449 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7700 (mtp180) REVERT: B 727 ASP cc_start: 0.7388 (m-30) cc_final: 0.7067 (m-30) REVERT: B 741 PHE cc_start: 0.6373 (m-80) cc_final: 0.6089 (m-80) REVERT: B 911 LYS cc_start: 0.7654 (ttmp) cc_final: 0.7121 (mtpp) REVERT: B 959 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8447 (tt) REVERT: C 56 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: C 101 TRP cc_start: 0.8857 (OUTLIER) cc_final: 0.7940 (m-90) REVERT: C 248 SER cc_start: 0.6964 (OUTLIER) cc_final: 0.6615 (m) REVERT: C 417 MET cc_start: 0.8760 (ttm) cc_final: 0.8337 (ttp) REVERT: C 433 THR cc_start: 0.7416 (p) cc_final: 0.6975 (t) REVERT: C 449 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7776 (mtp180) REVERT: C 514 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8187 (tttm) REVERT: C 546 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7618 (mt0) REVERT: C 643 ASP cc_start: 0.6820 (OUTLIER) cc_final: 0.6455 (t0) REVERT: C 877 GLN cc_start: 0.5552 (OUTLIER) cc_final: 0.5129 (tp40) REVERT: C 1020 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7958 (mmtp) REVERT: C 1085 PHE cc_start: 0.7262 (m-80) cc_final: 0.6944 (m-80) REVERT: C 1088 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6695 (pt0) outliers start: 76 outliers final: 49 residues processed: 318 average time/residue: 1.3611 time to fit residues: 498.6424 Evaluate side-chains 324 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 256 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 951 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 1032 MET Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1088 GLN Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.9990 chunk 177 optimal weight: 0.5980 chunk 137 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 304 optimal weight: 2.9990 chunk 280 optimal weight: 6.9990 chunk 242 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 192 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 B 181 HIS B 473 ASN B 827 ASN B1056 ASN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 473 ASN C 769 GLN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1040 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25059 Z= 0.173 Angle : 0.560 10.763 34047 Z= 0.305 Chirality : 0.044 0.225 3921 Planarity : 0.004 0.041 4359 Dihedral : 6.563 67.768 4092 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.78 % Favored : 96.16 % Rotamer: Outliers : 2.23 % Allowed : 18.33 % Favored : 79.44 % 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: -0.29 (0.14), residues: 3018 helix: 1.66 (0.20), residues: 726 sheet: 0.96 (0.19), residues: 657 loop : -1.65 (0.13), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 423 HIS 0.005 0.001 HIS B1046 PHE 0.016 0.001 PHE A1092 TYR 0.020 0.001 TYR A 367 ARG 0.003 0.000 ARG C1089 ********************** 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: 59 poor density : 259 time to evaluate : 2.694 Fit side-chains REVERT: A 122 ASN cc_start: 0.7588 (m110) cc_final: 0.7355 (m-40) REVERT: A 258 LYS cc_start: 0.7927 (mtpp) cc_final: 0.7607 (mttp) REVERT: A 546 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7646 (mt0) REVERT: A 554 ASP cc_start: 0.8106 (p0) cc_final: 0.7890 (p0) REVERT: A 932 ASP cc_start: 0.7270 (m-30) cc_final: 0.7014 (m-30) REVERT: A 959 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8225 (tt) REVERT: A 1088 GLN cc_start: 0.6689 (OUTLIER) cc_final: 0.5821 (mm-40) REVERT: B 258 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7402 (mmtp) REVERT: B 449 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7716 (mtp180) REVERT: B 727 ASP cc_start: 0.7352 (m-30) cc_final: 0.7018 (m-30) REVERT: B 741 PHE cc_start: 0.6313 (m-80) cc_final: 0.5951 (m-80) REVERT: B 911 LYS cc_start: 0.7593 (ttmp) cc_final: 0.7083 (mtpp) REVERT: B 959 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8411 (tt) REVERT: C 248 SER cc_start: 0.6636 (OUTLIER) cc_final: 0.6283 (m) REVERT: C 417 MET cc_start: 0.8784 (ttm) cc_final: 0.8418 (ttp) REVERT: C 433 THR cc_start: 0.7408 (p) cc_final: 0.6983 (t) REVERT: C 449 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7818 (mtp180) REVERT: C 514 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8157 (tttm) REVERT: C 546 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7520 (mt0) REVERT: C 643 ASP cc_start: 0.6690 (OUTLIER) cc_final: 0.6397 (t0) REVERT: C 797 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6565 (mtp-110) REVERT: C 877 GLN cc_start: 0.5430 (OUTLIER) cc_final: 0.5018 (tp40) REVERT: C 996 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.7969 (mtt180) REVERT: C 1020 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7967 (mmtp) REVERT: C 1085 PHE cc_start: 0.7238 (m-80) cc_final: 0.6947 (m-80) REVERT: C 1088 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.5848 (mm-40) outliers start: 59 outliers final: 40 residues processed: 306 average time/residue: 1.4339 time to fit residues: 503.4049 Evaluate side-chains 310 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 256 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 546 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 769 GLN Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 915 GLN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1088 GLN Chi-restraints excluded: chain A residue 1099 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 951 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 432 SER Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 514 LYS Chi-restraints excluded: chain C residue 546 GLN Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 631 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain C residue 795 THR Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 877 GLN Chi-restraints excluded: chain C residue 883 GLN Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 1020 LYS Chi-restraints excluded: chain C residue 1088 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 223 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 243 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 249 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 937 ASN B 181 HIS B 473 ASN B 827 ASN B 901 ASN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 473 ASN C 769 GLN C 827 ASN ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1040 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.142832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116238 restraints weight = 25731.482| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.66 r_work: 0.3041 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 25059 Z= 0.294 Angle : 0.698 12.929 34047 Z= 0.382 Chirality : 0.049 0.216 3921 Planarity : 0.005 0.044 4359 Dihedral : 7.098 62.969 4092 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.67 % Favored : 95.26 % Rotamer: Outliers : 2.53 % Allowed : 17.95 % Favored : 79.52 % 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: -0.53 (0.14), residues: 3018 helix: 1.25 (0.19), residues: 729 sheet: 1.00 (0.20), residues: 627 loop : -1.74 (0.13), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 423 HIS 0.010 0.002 HIS B1046 PHE 0.018 0.002 PHE B 316 TYR 0.030 0.002 TYR B 367 ARG 0.005 0.001 ARG A 829 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8548.54 seconds wall clock time: 153 minutes 8.90 seconds (9188.90 seconds total)